Major Rex Butler, a military intelligence man, and the psychiatrist John Henbest are in Henbest's office watching a girl on the couch. Neither awake nor asleep, she is talking about the man with whom she works and travels. She says they have been together for some years. Because she is young and pretty Henbest reads something dirty into the relationship but Butler disagrees. There is some hostility between the two men, partly explained when Butler claims to have been shot at earlier that afternoon. Henbest has given the girl an injection so that the pair of them can shed some light on this incident. Pliable to suggestion she tells them that her name is Ace. When asked about a man called Ray Morita she calls him 'Cosmic Ray' and claims to have only met him since arriving at the Hill in Los Alamos. The two men ask her about the Doctor. Her answers seem evasive but she is telling the truth: most people, including her, do not know where he comes from. She does, however, tell them that recently she visited the fishing station at Two Moons. They are perplexed to hear that this place was not on their planet. The Doctor's arrival in Henbest's office curtails their 'interview'. He pretends that Ace (he calls her 'Acacia') has merely fallen asleep and takes her away from her inquisitors. Butler is annoyed at their failure to elicit anything concrete from the girl and tells Henbest that there is a bomb to be built and a spy for him to catch.
Three days earlier: Major Rex Butcher realises that he has grown addicted to the chilli served by the Oppenheimers' Mexican cook, Rosalita, to the detriment of his waistline. He goes to pick up the two new arrivals at Los Alamos. He is in civilian clothing. The newcomers are Dr John Smith, an English physicist, and his associate, Acacia Cecilia Eckhart, or "Ace". He picks them up from the roadside out in the desert landscape. Believing Butcher to be their driver, the Doctor and Ace are more open in their conversation than they might have been. The Doctor reminds Ace to take her fish-oil capsule. Ace (who seems embarrassed about her clothing and is wearing a full-length raincoat) wonders if this is another caper like the one with Dr Judson. Eventually they realise that their driver is in fact Major Butcher, the man they thought he was taking them to meet. Ace is put off but the Doctor is impressed by the simple ruse which led them to be more open in his presence. The Doctor reveals that Butcher was once in the Pinkerton detective agency, and he also writes novels: Yellow City, Hell's Inheritance, and The Hawk of Gibraltar. The Doctor claims to be a fan, especially of Yellow City, for its complex depiction of labour relations and corruption. Despite himself Butcher is pleased, and also annoyed that Ace has never heard of him. Butcher drives them to the mesa above Los Alamos Canyon, Parajito Plateau; Robert Oppenheimer came here to convalesce as a teenager and suggested building the Manhattan Project here. Butcher drops off the Doctor and Ace near the Oppenheimer's house, where the Oppenheimers are throwing a party to celebrate their arrival. The Doctor has corresponded frequently with Oppenheimer who is impressed with him. Ace asks why they had to leave the TARDIS in Lamy and make a long journey by bus. The Doctor explains they needed to make their arrival seem genuine rather than just turning up out of the blue; he has fake train ticket stubs from Chicago to Lamy but has left the TARDIS close enough so that a friend can pick it up for them if it proves necessary. Ace is still coming to terms with their current location: when the Doctor said Los Alamos she thought he said they were going to the Alamo but this is the home of the Manhattan Project: Oppenheimer is calculating the critical mass of U-235, one of many scientists working to build the world's first atom bomb. While the Doctor and Ace attend the party Butcher goes through their belongings but finds nothing suspicious. Indeed, he finds proof that Doctor has read, enjoyed and annotated Butcher's novels.
The Doctor and Ace enter the Oppenheimer house where they find the guests drinking martinis and cigarette smoke is thick in the air. Classical music is being played on the record player. Robert Oppenheimer greets them and his wife Kitty, already drunk, offers to take Ace's coat - she has it unbuckled before Ace can protest - to reveal Ace is dressed as a cowgirl, classic Annie Oakley style. She thought they were going to the Alamo, not Los Alamos. The drunken Ray Morita leers at her and steals John Henbest's drink. A few drinks and bowls of chilli later however Ace is no longer so humiliated. Kitty is irritated by Morita's hep-cat attitude and groovy Indian clothing. She tells Ace she is proud she married Robert, her fourth husband, and got him out of the clutches of Jean Tatlock's bad crowd. Butcher belatedly arrives at the party and Morita then spots Ace again and makes a drunken pass at her. When Professor Klaus Fuchs starts playing the Liebestod from Wagner's Tristan and Isolde a disgusted Morita storms out. Butcher also disapproves of the choice of music, though the Doctor points out that Wagner is not in fact Hitler's favourite composer, that dubious honour going to Franz Lehár, composer of light operettas. He tells Ace that Morita is a third-generation Japanese-American whose family are in internment camps. Morita is only permitted to work there because his scientific genius is deemed necessary to the war effort. The Doctor and Ace witness an argument between Oppenheimer and Hungarian physicist Edward Teller, who believes that the atom bomb will ignite a chain reaction that will incinerate the entire Earth's atmosphere. Ace is relieved that this didn't in fact happen but notes that the Doctor does not respond when she says this. Morita returns with a bag of needles and a large yellow leather bag used for holding records. He tosses the Liebestod aside, causing it to shatter on the wall, to Fuchs' outrage. He then replaces it with Duke Ellington's Jump for Joy, released in 1943. He ostentatiously plays it with a different needle, claiming that the old one was worn out and would have destroyed the record. As the others dance to the music, the Doctor watches carefully as Morita relates every minute detail of the recording of the album, almost in tears that such beautiful music was nearly lost forever.
The next morning finds Ace employed performing mathematical calculations for Abner Apple, a scrawny and angry scientist. She is supposed to be doing his "donkey work", taking the load off to save him time so that he can concentrate on more theoretical work. Really she is supposed to work for the Doctor but he is at his security interview with General Groves and Apple grabbed her the moment she left the breakfast table. Unfortunately she did not have the chance to take her fish-oil capsule and the equations are proving well beyond her mental capabilities. She extemporises, claiming she needs to return to the WAC barracks to attend to "women's business." Apple is too embarrassed to pry but follows her, convinced that she is not a mathematical prodigy at all but is sleeping with the Doctor. Butcher spots them and follows. Apple complains to him about what's "really" going on but Ace gets into the women's barracks before either of them catches up with her and takes her capsule. As a result, when she returns to the laboratory (again followed by the suspicious Butcher), she is able to perform mathematical equations quickly and precisely. Apple is at first astonished, then overwhelmed, and finally infatuated (Ace may have traded one problem for another). The Doctor arrives and collects Ace, Apple protesting to no avail. Realising what nearly happened he reminds Ace of the importance of taking her capsules, the oils in the alien fish's liver (obtained from the fishing tribe at Two Moons) have an effect similar to omega lipids in the human brain, boosting the ability to perform quick and accurate complex mathematical calculations, so that she will be accepted as the Doctor's mathematical assistant. The Doctor leaves Ace again in order to speak with Teller. He asks Ace to befriend Morita and again doesn't reassure her that it's not possible for an atom bomb blast to destroy the world.
Ace visits Morita's apartment and hears him playing a jazz record. He is surprised to see her and makes a fumbling attempt to hide a picture, framed and autographed, of a beautiful Japanese woman named "Silk". Ace is sympathetic towards Ray because his family has been locked up just for being Japanese, but for a moment it is almost as if he doesn't understand what she is talking about. He offers her a cold beer but before she has had time to drink any of it there is a knock at the door. Ace doesn't see who it is but Ray returns to the front room with a new record, and makes a clumsy attempt to hide it, claiming that he has to clean it before playing it. Almost immediately afterwards Butcher arrives and holds Morita at gunpoint, demanding "it". Butcher orders him to play the new record, which confirms that it is sung by Lady Silk. Butcher then confiscates it. Lady Silk is Japanese-American fifth columnist who spreads propaganda to destroy morale, or so Butcher claims. He kicks Ace out of the apartment. Downstairs Ace meets the Doctor and quickly fills him in concerning these events. As they leave the building someone shoots at them and they take cover. Butcher rushes out, gun drawn, and sees the Doctor and Ace but they claim they didn't hear anything. Butcher was reacting to the sound of gunfire and since he is obviously suspicious of both the Doctor and Ace but does not stop to interrogate them it indicates that he knows they are not connected to the investigation he's currently pursuing. The Doctor buys Ace dinner at Fuller Lodge, briefly interrupted by Apple who now has a schoolboy crush on Ace.
The next day Ace takes her fish oil tablet and she and the Doctor work all day on equations. The Doctor explains that he is not actually changing history, just doing enough to be seen as valued member of the team. Noticing that Ace is hungry, the brain having burned many calories, he takes her to the Oppenheimer house where he has arranged for a late meal to be provided: their cook, Rosalita, has made them some of her famous chilli. Rosalita is happy to provide it but when the Doctor casually mentions that he and Ace will be sharing it with Cosmic Ray, Rosalita seems shaken and accidentally drops the casserole dish, spilling the chilli over the floor. The noise attracts Kitty Oppenheimer, and they chat with her while Rosalita warms up some leftover chilli from the party. On the way, Ace asks the Doctor about the Jean Tatlock that Kitty had mentioned earlier. She was Oppenheimer's former flame, a woman with subversive friends, but Oppenheimer foreswore all connections to them when he started work on this project. The Doctor and Ace stop by Ray's to share the chilli, and Ray plays his Duke Ellington records for them. He uses cactus needles, each one can only be used once, so as not to damage the vinyl but they are difficult to come by even out in the desert. The Doctor asks why Butcher would bother showing up with a gun to confiscate the record, and Ray reveals that Butcher thinks he's a spy and that there are coded messages on the discs. On their way back to their respective barracks, the Doctor explains to Ace that despite Oppenheimer foreswearing his political connections Oppenheimer and Teller will become mortal enemies after Teller testifies against him to the US government. Furthermore, Ray Morita used to be an ordinary high-school teacher, not a physics genius, and he also used to be left-handed. Someone is interfering with history and trying to destroy the human race.
The following day Ace is once again performing more fantastically complex calculations when Apple slips her a note asking her to the movies. The Doctor takes Ace to the Oppenheimers' residence to investigate his suspicions and they find Oppenheimer burying a dead rat. He tells them that he has given Rosalita the afternoon off. Concerned, the Doctor takes Ace to Ashley Pond to look for Rosalita but finds Butcher trying to arrest Ray and Private Dobbs (who has been smuggling in contraband). Ray insists it is a mistake and the Doctor tests a theory by opening Dobbs' rucksack and finding not Lady Silk records but cactus needles. Butcher, disgusted, sends Dobbs on his way, but Ray is upset because it will take him forever to find another supplier. Someone starts to shoot at them from a copse nearby. Butcher returns fire and the Doctor rushes to investigate with him. He returns with a record and tells Ace to hide it. Butcher emerges shaken from the copse. He shot and killed the gunman... or rather woman, because the corpse is that of Rosalita. The Doctor assures him that he had no choice but Butcher feels terrible about shooting a woman. Ace deduces from all this that it was Rosalita who was bringing in the illicit records for Ray and that she must have been at his apartment the previous day and shot at them. The Doctor says he suspected her after the previous night but is unable to explain further because they are interrupted by Dr Henbest calling them in for their psych profiles. Before he can start asking them questions he is called in about the shooting. Ace now demands answers from the Doctor who explains he does not yet want Butcher to know that there is a positive link between Rosalita and Cosmic Ray. He does, however, explain that he suspected Rosalita after she prepared chilli for them and then spilled it when she learned Ray would be sharing it - the same chilli that ended up in the garbage can where Oppenheimer found the dead rat, poisoned. Ace asks why he doesn't want to turn in Ray but the Doctor doesn't answer; he leaves for another meeting with Teller, still hoping to convince him that his calculations are wrong and that the atom bomb will not destroy the planet, though again he does not reassure Ace that this is in fact the case.
Ace remains resting in Henbest's office, on the only comfortable chairs in the whole base. She is shaken by the day's events. Henbest returns and notes a rash on her arm which he says could be first signs of radiation exposure but while Ace is looking for it he injects her with contents of a syringe. Butcher arrives. Ace can't resist as Henbest gives her further injections.
She wakes up to find that the Doctor got her out and took her to Cosmic Ray's to sleep it off. The Doctor and Ray Morita have been discussing physics. Ray confirms that Rosalita was going to give him the record and that he arranged to meet Dobbs at the same time, but he didn't know she would start shooting. Nevertheless, Ace refuses to let the Doctor leave her alone with him and accompanies him out, though still woozy. She is upset that the Doctor gave the record to Ray, but he has his reasons. In the meantime they pay a visit to Henbest. The Doctor shoots him in the neck with a dart from his umbrella, injecting a toxin into his bloodstream, causing Henbest to hallucinate and become susceptible to suggestion. Ace has fun manipulating his hallucinations until he nearly drowns believing he is a tuna fish. The Doctor then hypnotises him to believe both he and Ace passed their psych evaluations with flying colours. He also asks about Lady Silk, Imperial Lee and the Rising Sun Apocalypse Commandos, but Henbest has never heard of them. Ace asks why he does not use that drug to change Teller's mind. He replies that would be gross interference with a man's mind and brain. The Doctor only did it to Henbest because he was angry. Ace now wants answers, and the Doctor explains that Ray, though in league with their enemies, is not too bad in himself, he is merely being used.
They return to Ray's and find him listening to Lady Silk singing a song called "Nagasaki". Butcher was correct; Silk is indeed slipping coded messages to him. However, he is not a very good spy and he has been making notes which the Doctor now takes. The Doctor also tells Ace that while chatting with Ray earlier he determined that Ray's knowledge of particle physics is far too advanced; this Ray is not this universe's Ray Morita, but a particle physicist from the twenty-first century in another timeline. Butcher arrives so the Doctor tosses the record out the window before Butcher can enter. He claims that he and Ace are here to talk physics with Ray. He catches Butcher off guard by reminding him he has every reason to be upset since he killed a woman, and offers him a beer while they discuss his novels. Butcher, rattled, storms out and only when he gets home does he realise that the Doctor had named a novel, Shadow Man, that only exists in outline form -- and he only recently thought up the title and hasn't written it down anywhere.
The next afternoon Butcher visits the Oppenheimers to tell them personally about Rosalita's death. Kitty accuses him of murder. He blames himself. When Oppenheimer tells him that he's given Dr and Ace some time off to look at fossils and that Ray has accompanied them into the desert, Butcher becomes suspicious and decides to follow. Butcher has trouble requisitioning a Jeep but eventually sets off after them. The Doctor, Ace, and Ray are out in desert. Ray didn't bring records, afraid the dust can damage them. The Doctor is leaving Teller to ponder his arguments. The Doctor drives them out to a hill slope where three men with guns are waiting. The Doctor greets them by name: Black Eyes, Scar and Sun Runner. They are Mescalero Apaches, those who harvested the wild mescal and peyote plants, cactus with hallucinogenic properties. Sun Runner builds a fire in the mouth of a cave. Butcher drives until it gets dark, losing the Doctor's trail, but then sees a light in distance. He stops his Jeep and closes in on the light of the fire but Sun Runner is tracking him and forces him to the fire at gunpoint. The Doctor greets him and Butcher realises that the Doctor had the fire built to lure him. Or rather, the Doctor claims, so that Butcher didn't tire himself out with wasted wandering around the desert in the dark. Ray is sleeping. The Doctor offers Butcher a drink of mescal and a sandwich which, after Butcher eats it, the Doctor claims contained peyote; now they're waiting for it to take effect. Apparently it does, because when Butcher looks up he sees a flying saucer hovering above them. The Doctor waves his hat to the saucer, which is more like a big floating jellyfish; it produces boarding tubes like tentacles and sucks the Doctor and Ace aboard. When Butcher's turn comes he struggles in a panic, resisting. He is obviously experiencing culture shock, never having experienced anything to prepare him for this. The Doctor admits to Ace that the sandwich actually contained guacamole; he just let Butcher think it contained peyote as a get-out clause in case he could not handle this experience. He speaks roughly to Butcher, bullying him into pulling himself together, explaining this is a flying ship of the kind called "foo fighters" by air force pilots. The Doctor and Ace go to meet the pilot. Butcher, still in denial, stays right where he is. Ace is contemptuous but the Doctor reminds her that this is entirely out of Butcher's experience. Through the translucent skin of the craft Ace sees another tentacle lower and bring someone else aboard; it's Ray, and Butcher, even more disgusted with him than bewildered by the ship, joins the Doctor and Ace rather than let Ray wander off alone. He is starting to acclimatise, but with difficulty, and he loses his mental equilibrium when the Doctor introduces him to the ship's pilot, Zostrathnia Otocr Regus Gelb, or Zorg, who resembles a giant jellyfish-crab. This proves too much for Butcher to take, at which the Dr gives in and reminds him of the peyote, using light hypnotism to send him to sleep. Ray, who has drunk too much mescal, passes out. The Doctor asks Zorg to send the unconscious duo back to the ground, announcing that the Apaches will drive them back up the mesa where the Los Alamos authorities will find them apparently having slept off a drunken night. In the meantime Zorg has brought the TARDIS for the Doctor and Ace: the time has come for them to take the fight to their enemies by going in search of Lady Silk. Since they can't risk being found missing at Los Alamos they'll use the TARDIS to return by going back in time once their mission is accomplished.
Butcher awakes the next morning with pounding hangover, convinced that the Doctor got him drunk and slipped him peyote, but the story sounds ridiculous even to him. The Doctor, Ace and Ray have returned to Los Alamos of their own accord, but when a furious Butcher confronts him the Doctor claims that he and his friends just went out to meet the Apaches, Butcher stumbled across them, all was resolved and they spent a friendly night eating and drinking. It is only Butcher's word against the Doctor's. Furious, Butcher notes that Ace is wearing sunglasses. When she removes them she reveals she has a black eye but does not say where she got it. Butcher storms out and runs into Oppenheimer who reports that Ray has gone missing after returning the Jeep. Butcher is unable to pursue his vendetta against the Doctor without evidence and must drop it for now, going instead to look for Ray. The Doctor and Ace already know where Ray is, but they couldn't bring him back with them when they returned back through time because it is necessary for Butcher to go looking for him.
The Doctor and Ace, who have just returned from Zorg's ship, have bought a train ticket to Los Angeles. When Ace learns that Duke Ellington is on the same train she recognises that this fact, conjoined with Ray's respect for his music, is more than a coincidence. The Doctor confirms that he wants to have a chat with the Duke which occurs over the Duke's incredibly large breakfast. The Doctor quickly impresses the dapper man with his knowledge of Ellington's ensemble and the changes that have taken place in it but he is particularly interested in a former singer who now goes by the name of Lady Silk. Duke remembers her well, a beautiful young woman with a wonderful singing voice, who didn't seem particularly political but turned to treason overnight. Under the impression that the Doctor is a federal agent, he agrees to help (despite his fondness for Lady Silk he does not agree with her turning traitor). He suggests that the Doctor check out a particular cult; California seems rife with them and Lady Silk seemed particularly interested in this one.
The TARDIS was in the train's baggage compartment. After speaking with Duke, the Doctor and Ace use it to travel to the grounds of the cult he mentioned: the Chapel of the Red Apocalypse. It is a quiet Mexican-style house. The gate is unlocked and there is an astronomical observatory on the roof. A man named Albert introduces himself as the caretaker; he and his wife Elina are looking after the place while its owners, the Storrows, are "away," having apparently gone to Mexico and abandoned the temple in the house's basement. Apparently they mixed with many famous names. Albert shows the Doctor and Ace a photo album, and they recognise a photo of Lady Silk. Albert is delighted to help them catch the traitor. He offers to show them the Storrows' correspondence and the ledgers containing private information about the other members of their cult. The Doctor sends Ace to check out the ledgers, and on the way up with Albert they pass through a hall with framed photographs. Too late Ace notices that the photos are of Albert and Elina posing with celebrities, including Lady Silk and, before she can react, Albert knocks her down and beats her unconscious.
She recovers to find that she and the Doctor have been tied to chairs in the observatory. Twenty four hours have passed. The Storrows (Albert and Elina) repeatedly administered chloroform to her whenever she threatened to wake up. Now that she is awake the Doctor urges her to knock over the telescope and break the lens so that they can use broken glass to cut themselves free. However, Ray arrives, having gone AWOL from Los Alamos to hear Duke play live, and he is upset to see that the Doctor and Ace apparently came looking for him at the cult's headquarters. The Doctor didn't actually know that Ray would be coming here though he does know that he is working with Lady Silk and Imperial Lee. He asks Ray to explain why, and in the process reveals to Ace something else he's not told her: while Ray comes from a different dimension than this, it is from Ace's own. The Doctor and Ace are currently in the alternative dimension. Ray used to be a particle physicist, working on quantum equations so far out that they were almost like magic. The possibility that a particle accelerator could bring into existence esoteric energy particles that could destroy the entire planet is very, very, very small. Nevertheless, as Ray worked he came to believe that the equations themselves were part of the possibility, and solving them made it more likely. Lady Silk and Imperial Lee somehow found out about his theory and convinced him that human desire was part of the equation. They can use the calculations to pass over into another dimension but desire is necessary to bridge the gap. As the Doctor realised at the party, when Ray talked of how easily this music could have been lost, the desire was Ray's for the music of Duke Ellington. In Ace's timeline the musician's union was on strike for two and a half years which coincided with the Duke's greatest period when his best band was together. As a consequence none of that music was recorded. In the alternative dimension the strike did not occur so Ray came here, bringing Lady Silk and Imperial Lee with him. Their plan is to destroy the world. Ray knew there would be a price but didn't know just how bad it would be. Now that he does know he is still is willing to pay it for these records.
Lady Silk arrives in the astronomy room. She is disappointed to see Ray talking with the prisoners. She cuts them free, and though the Doctor overpowers her and takes her knife, she isn't concerned. The Storrows are behind her with sub-machine guns. They take the Doctor and Ace to the chapel in the cellar. The floor is tiled to resemble the post-war Japanese flag with a well in the centre, the "Well of Transition", where Ray, Silk and Lee arrived in this dimension. Imperial Lee is here, too. He has renamed himself: in his original dimension he was called Stanley Wainwright. He and his followers are kamikaze soldiers on a mission to alter the outcome of the Los Alamos project. With Cosmic Ray's help they'll use the quantum equations to trigger a chain reaction, bigger than ever Teller feared, big enough to destroy the universe. The effect will ripple out through the multiverse, tilting history in all worlds so that the Japanese win World War II. Lee and his followers will remain behind to ensure that the plan succeeds, but Silk will return "home" to a world now ruled by the Japanese. Lee requires reinforcements and to make the link from this side he intends to let the Storrows sacrifice the Doctor and Ace. Ray protests but the Storrows recount how they were in the process of sacrificing a sheep when Ray, Silk and Lee arrived. They believe that at this level spells and equations are, to all intents and purposes, the same thing.
Ray reluctantly begins to write the equations on the floor, but then the doorbell rings. It is Butcher. He has used his contacts in the Pinkerton agency to track Ray to this place. The Storrows go to greet him, playing caretaker and wife again, but they are a bit nervous and Butcher sees through their lies. He pretends to believe it and leave, but circles around, back to the house. Butcher creeps to the house, listening at cellar window. He overhears Silk and Lee preparing to sacrifice the Dr and Ace to bring reinforcements from their world. When the reinforcements arrive their duplicates will be drawn to them and there will be more bloodshed, just as before. Ray is sickened but continues to write the equations. Butcher, not fully understanding but knowing these people are subversives, and that the Doctor and Ace are in danger, prepares to make his move. Elina finds him, having realised that he knew they were bluffing. She attacks him with an axe. Butcher defends himself with a garden hose. He swings it like rope and hits her in the face with the large brass nozzle, then on the back of the head, knocking her out. He ties her up with the hose.
The Doctor is trying to gesture towards Lady Silk but Ace doesn't understand what he's trying to tell her. Ray is protesting that this process does not require anybody's death. He insists that they are fooling themselves into believing they can destroy the universe but Silk knows he's in denial and that the real reason he quit his job at the particle accelerator in their own dimension was because he came to fear his own equations. He felt that the calculations used to predict the death particles would be part of the process that brought the death particles into being. If he performs the calculations near the atom bomb test, it will trigger the apocalypse. The Doctor and Ace are to be sacrificed but Ace finally realises that the Doctor is reminding her he took Lady Silk's knife. Ace steps behind him and he puts the knife to Silk's throat. Butcher enters the building and finds Elina's robe. Lady Silk is unconcerned because she knows the Doctor won't cut a defenceless woman's throat. So he trades places with Ace and gives the knife to her. Now Silk is worried. While they are all distracted Elina enters... or so they think until "she" gets close and reveals herself as Butcher in disguise. Butcher shoots two of Lee's henchmen, one convulsively fires his machine-gun as he falls, cutting down the third and Albert. In the shocked moment afterwards Silk and Lee leap into the Well of Transition. Butcher pulls the sobbing Silk back out, ignoring her claims that she was held prisoner here for days but the Doctor points out she is wearing different clothing. Lee is dead, but not hit by a ricochet; he has been dead for days and he too is wearing different clothes. These are not the same Silk and Lee that just threatened the Doctor and Ace: this is the Lady Silk from this dimension, an innocent victim replaced by her own doppelganger. Butcher concludes that the Doctor is disoriented after being doped up by the Storrows and places Silk under arrest.
The Doctor and Ace somehow give Butcher the slip and then end up back at Los Alamos. The capture of Lady Silk is treated as if it was a military operation, and with Silk in custody everyone scrambles to get a piece of the glory. Butcher's role in things is all but forgotten. Elina Storrow has been locked up in a mental institution and somehow Imperial Lee's body has gone missing in the confusion. The Doctor produces papers showing him to be an undercover British agent. Since he and Ace and Ray are necessary for the test they are put back to work, to Butcher's anger. The day of the Trinity test draws near, and someone has the bright idea to bring in Lady Silk as a prisoner for propaganda morale boosting; though she's a cowed and frightened girl, not the confident woman from the cellar, and insists she was kidnapped and held prisoner and never betrayed her country. Butcher is placed in charge of guarding her. :
16 July 1945, 4:00 a.m.; Butcher is holding Silk in his hut, waiting for her to be picked up, when the Doctor calls him: he's at Ray Morita's apartment and he has important information about the missing body of Imperial Lee, which he will only tell Butcher if he brings Lady Silk. Butcher gives in and does so. As soon as he arrives at Ray's apartment he is held at gunpoint by Imperial Lee, not dead. The Doctor repeats his assertion that the dead man was this world's Lee, and this is his doppelganger from another dimension. Lee claims it was synchronicity and magic that brought Lady Silk to him tonight. Ray brought Lee back with his equations but Lee needed Silk's double here to bring her back as well. Before Butcher's eyes Silk is suddenly wearing entirely different clothing and her demeanour has changed. Lee is triumphant. At 5:29:45 a.m., Monday 16 July 1945, Trinity will be tested. The Doctor stops Butcher from interrupting, telling him that it is impolite. Ray has written the equation, just missing the final formula. Lee orders him to write it down at the very second Trinity is detonated at which point the equations will become part of the probability equation, the death particles will come into existence, and this entire universe will be destroyed. Lady Silk is just here to see the start of the fireworks, and then she and Ray will go home, Ray taking his records with him. Lee gives the gun to Silk as he paces. The escape equations are ready. They count down to the critical moment, and at precisely the correct moment, Ray completes the equation. And nothing happens. The reason is that this is a different dimension, and Trinity is scheduled to detonate the next day at 5:00 a.m. precisely. Lady Silk is furious, but while she's distracted, the Doctor fires a toxin dart from his umbrella into her neck and Ace grabs the gun. Lee, realising he's lost, leaps to his death from the second-storey window. Now Butcher has an open-and-shut case, and the Doctor agrees to let him take the credit on the condition that he clear Lady Silk's name, and avow that she was an innocent victim held prisoner and terrorised by Lee. To prove his point he takes the escape equation from Ray and puts it in Silk's fingers. Suddenly she is not paralysed any more and is wearing the same clothing she wore when they arrived. She is begging Butcher not to send her back to that terrible place. Butcher gives in, and the Doctor explains that he had Ray summon Lee and the other Silk here so that Lady Silk could witness Lee's humiliating failure and take the story back to the rest of their people. The threat to the multiverse is over.
The Doctor explains to Ace that his equations cast some doubt on the geometry of Kistiakowsky's explosive lenses, and the test was delayed a day thanks to him. The Doctor, Ace and Ray witness the atom bomb test from Zorg's ship. The Doctor admits that Teller stuck to his incorrect beliefs right up to the end, and when he was proven wrong, he was humiliated and became a proponent of nuclear arms. In fact he became too much of one; he discredited Oppenheimer and advocated nuclear weapons, building them bigger and better, and starting the world on the road to nuclear proliferation. The Doctor had hoped to change that, but recognises it may have been too much to expect. That was actually his real mission in this dimension He had never believed Lee and Silk could succeed in their plans, but he had to try anyway, just in case. He tells Ace that they are finished here and that they can return to their home dimension. They will be taking Ray with them and he will have his precious records.