Mexico City, 1994. The Doctor, Ace, and Benny respond to a call for help from Cristian Alvarez, a man who knows them very well although they have never met him before. A few months ago, a gun-wielding lunatic shot up the local marketplace, and before he was shot Cristian saw that the man was possessed by the Blue, a psychic force Cristian has encountered three times before. On two of those occasions, the Doctor and his companions were there -- but due to the vagaries of time travel they have intercepted his call for help before their first meeting. The Doctor tries to hypnotise Cristian to find out what he saw, but Cristian is too traumatised to remember anything. The Doctor and Benny therefore research Cristian’s 1978 sighting, the one at which they were not present, and learn that it coincided with the unearthing of the Aztecs’ Great Temple by construction workers -- and with a wave of madness which affected many Mexicans with native blood. One of the victims, the famed psychic Nahualli, never recovered. The Doctor visits the mental hospital where Nahualli is being held, while Ace goes to the marketplace to investigate the gunman’s rampage. While there she triggers a psychic boobytrap meant for the Doctor, and the psychic energy flings her aside and tracks down the Doctor; he evades the attack, but the dispersing energy kills Nahaulli and a passing attendant.

The Doctor, believing that the Blue originated in the Aztec Empire, decides to visit Tenochtitlan in 1487 AD. Cristian, however, is in no shape to travel through time, and the Doctor thus tells Benny to stay with him in case he is attacked again. Before leaving, the Doctor contacts his old friend Lawrence Fitzgerald, a professor at the local university; while she’s here, Benny might as well research Aztec history and try to learn something about the enemy. Fitzgerald allows Benny to use his own research notes, and offers to show her some of the rarer Aztec written documents, few of which survived the purge by the Spaniards. In the course of her research, Benny finds references to Huitzilopochtli, a god whose existence may have been inspired by a real figure from Aztec history. The Aztecs believed that hummingbirds were the reincarnate spirits of fallen warriors, and placed south to the left on their maps; the name Huitzilipochtli translates literally to “left-handed hummingbird”, or “warrior from the south”. Benny returns to Cristian’s home to review her notes, but Fitzgerald unexpectedly attacks her in the apartment lobby -- and although she overpowers him, she then beats him to death in a frenzy. Cristian must call the hospital and have the raving, possessed Benny taken away for her own safety.

Upon arriving in Tenochtitlan, the Doctor and Ace find and rescue young Iccauhtli, who has been condemned to death for missing a drumbeat during the emperor’s coronation. They try to get him to sanctuary at the temple, but encounter the emperor himself on the way; fortunately, he assumes the white-skinned Doctor to be the god Quetzelcoatl, and thus absolves Iccauthli of all blame. Iccauhtli’s grateful father, Ce Xochitl, offers to introduce the Doctor to his other son, the priest Achtli; however, when Achtli arrives at his father’s home he attempts to kill the Doctor. The Doctor overpowers and hypnotises him, and learns that Achtli was told to kill him by the Blue. Achtli takes the Doctor and Ace to a sacred cave where it is said that Huitzilipochtli killed his sister Coyolxuahqui with the “turquoise serpent”, the magic weapon called xiuhcoatl. On the way, they are attacked by bandits -- and Ace discovers that the Doctor has removed the bullets from her gun without telling her. She and Iccauhtli overcome their attackers in any case, and the Doctor continues on alone to the cave while they guard his back. At the cave, he finds the remains of a crashed Exxilon spaceship’s power core, leaking radiation in lethal quantities as its shielding deteriorates. But he is still no closer to learning the true identity of the Blue; all he knows is that within days, twenty thousand warriors will be sacrificed to the newly constructed temple -- the temple which sent a psychic shockwave through all those of Aztec descent when it was unearthed in 1978.

Ace is angry with the Doctor for removing the bullets from her gun, particularly when she realises that he did so not to protect her from the Blue, but from herself. She is also displeased to learn that he intends to let the mass sacrifice proceed, as it is a natural part of history. He is aware that he will have to deal with her mistrust, but he decides first to deal with the Blue by taking the mushrooms which Aztec priests such as Achtli ingest during their sacred rituals, in order to see what he is facing. He is confident that his Time Lord metabolism will allow him to perceive his enemy and then break down the psilocybin without harmful effects, but he orders Ace and Iccauhtli to remain on guard in case their enemy tries to attack while his guard is down. Achtli remains with the Doctor to guide him through the trip, while Ace and Iccauhtli stand guard outside -- but Ace allows herself to be provoked by a taunting gang of warrior youths, and attacks them. By the time she comes down from the combat high things have gone horribly wrong; Iccauhtli has been killed by the gang, Achtli has died of a psychic haemorrhage, and the Doctor, unable to control himself, has rushed to the Temple -- where the Blue pushes into his overly receptive mind, and he is unable to keep it out. When he recovers, 24 hours later, he has learned nothing and both of Ce Xochitl’s sons are dead.

The Doctor and Ace return to Mexico City, where Benny has recovered and has been released from hospital with surprisingly little police involvement. She has, however, been barred from the university, and the Doctor concludes that the Blue sent Fitzgerald to stop her from studying the surviving Aztec codexes. He, Ace, Benny and Cristian break into the university museum after hours, but find a man named Macbeth waiting for them with a gun; he has been hunting the Doctor since 1968, and he arranged for the police to leave Benny alone so he could trap the Doctor and question him about the deaths he caused over 25 years ago. Ace overpowers Macbeth and holds him back while the Doctor examines a reproduction of the Codex Atlaca -- but as he begins to read it, a powerful psychic blast incinerates Macbeth, and the Blue appears in the museum in the form of a ghostly Aztec warrior. Cristian tries to flee with the Codex, but the Blue sweeps through him, consuming him and burning the Codex to ashes.

The Doctor takes Benny and Ace back to the TARDIS; they need Cristian’s help to detect their enemy, and that means going back to 1968 to find out what happened the first time he saw the Blue. They find young Cristian wandering the streets of London on a bad acid trip, and take him back to the home he shares with John, Elizabeth and Molly. John and Elizabeth thank them for helping Cristian and invite them to their Christmas Happening, but Molly seems horrified by the sight of the Doctor, and as soon as she gets the chance she slips away to speak with Lieutenant Macbeth of UNIT’s new Paranormal Division. Macbeth had visited their home earlier to investigate reports of a possible haunting, and he’s about to dismiss it as hippies on LSD when Molly arrives. A devout Christian and mild psychic, she has dreamt of the Doctor’s arrival and his transformation, and she believes that John and Elizabeth plan to summon the Devil. Macbeth breaks into their house, where he finds an Aztec calendar in the cellar, pinned above a bed with handcuffs attached to it. The Doctor has checked into a nearby hotel, and Macbeth goes to question him -- but is forced to shoot Molly, who had arrived there first and was trying to stab the Doctor to death.

By now, Benny has guessed what is happening, and the Doctor is forced to admit that she may be right. The hummingbird requires massive amounts of food to survive, and the Left-Handed Hummingbird is no different; even with the psychic energy fed to it by the Aztecs’ sacrifices it would have dissipated eventually. But history has been changed yet again, and it has anchored itself -- within the Doctor, who was possessed during his trip in Tenochtitlan. He was attacked in the University museum, not by the Blue, but by the Codex Atlaca, a storehouse of psychic energy which sensed the Blue within him… and he’s afraid to tell Ace, for fear of what she might do to him. He attends the Happening with Ace and Benny in order to speak with Cristian, a natural psychic whose mind was opened to the Blue by his LSD trips. Cristian sees the Doctor as an ixiptla, the avatar of the god. Desperate to know what has happened to him, the Doctor takes more LSD with John and Elizabeth, and allows them to handcuff him to the bed in the cellar. Benny realises that her hosts have drugged Ace, and when Cristian starts to channel the Blue again, she flees to fetch reinforcements. By the time Macbeth arrives, however, the Doctor is unconscious, Cristian is catatonic with terror, and John and Elizabeth have vanished…

Macbeth offers to take the Doctor to hospital, and when Benny admits that the Doctor isn’t human Macbeth immediately has him taken away for study. It takes Ace and Benny three weeks to track him down, and for those three weeks the Doctor is held prisoner in an experimental facility where scientists run tests on him. But traces of the drug remain in his system, and every four hours he suffers an acid flashback which strengthens the enemy’s hold on him; for a moment he fades from existence, and a psychic storm wreaks havoc amongst the sensitives of Britain. Ace and Benny eventually locate him, break him out and send word to their contacts in UNIT to have the division closed down. This is the end of Macbeth’s career; he will spend the rest of his life as an outsider, investigating without participating, growing ever more bitter and angry, while the touch of the Blue he encountered awaits its chance to burst out of his body in Mexico City.

Benny and Ace take the Doctor to Allen Road, where he identifies the Blue as the spirit of the Aztec warrior Huitzilin. Huitzilin’s natural psychic ability was amplified by exposure to the radiation from the crashed spacecraft, and he developed the power to feed on the death of his enemies -- but the more he eats, the more he needs to survive. He destroyed his rival sister and her followers with the xiuhcoatl, a weapon scavenged from the spacecraft, and thus became ruler of the Aztecs and drove them on to greater conquests. The Aztecs continued to sacrifice to him after his physical death, but eventually he would have dissipated… were it not for the Doctor, and the interference of the enemy who made the Silurian Earth and resurrected the Garvond. It was Huitzilin who drove the Doctor to the Happening, where John and Elizabeth tried to summon a god to bring meaning to their lives. Huitzilin devoured them, and his hold on the Doctor grew stronger still. Soon there will be no Doctor at all -- just Huitzilin, free to feed.

Huitzilin possesses a passer-by and attempts to assassinate John Lennon at the Beatles’ rooftop concert, to increase the panic and despair in the world and provide himself with more psychic energy. Ace saves Lennon, but the Doctor fears that Huitzilin may have influenced the Helter Skelter murders in response. Cristian is too traumatised by his experiences to help them now, and the Doctor therefore takes Ace and Benny to New York City in 1980, and their second destined meeting with Cristian and the Blue. Cristian has come to the city for a vacation, but is too frightened to leave his hotel room, and the Doctor realises that Cristian’s psychic ability drew him here to witness the coming of the Blue. The Doctor seems to lose interest and goes out for a walk, but the suspicious Ace follows him -- to the Dakota apartment complex, just in time to see Mark Chapman kill John Lennon. Huitzilin has forced the Doctor to bring him here in order to feed.

Cristian is once again traumatised by the psychic backlash when Huiztilin feeds, but this time he accepts the Doctor’s claim that he will never be free of his fear unless he faces it. Benny does some research and finds that the last surviving complete copy of the Codex Atlaca went down on the RMS Titanic, and the Doctor decides to recover the Codex, hoping to use the stored psychic energy within it to destroy Huitzilin forever. Cristian agrees to accompany him, but as they set off, Ace is possessed by Huitzilin and stabs the Doctor in the chest. He pretends to die so Huitzilin will release his hold on Ace, but Ace falls into a coma. Benny remains with her in the TARDIS sickbay while the Doctor and Cristian set off to confront Huitzilin -- but neither she nor the Doctor is sure whether the attack was motivated more by Huitzilin, or by Ace herself.

There are only hours to go before the Titanic’s fatal iceberg encounter, but fortunately Cristian is contacted by a young woman named Anna who believes he is the contact through whom her father intends to sell smuggled Aztec artefacts. Cristian gives her message to the Doctor, but the Blue beats them to the rendezvous and consumes both Anna and her father. Anna tries to shoot Huitzilin as he approaches her, but the bullets pass through his insubstantial form without effect. The Doctor confronts Huitzilin, realising that just as he came for the Codex, Huitzilin came for another of the smuggled artefacts -- the xiuhcoatl. The triumphant Huitzilin informs the Doctor that he did not cause the death of John Lennon, or any of the others, directly; the human race did that all themselves, and Huitzilin was just along for the ride. The Doctor tries to use the Codex to rid himself of Huitzilin, but they are too closely linked, and the pain is too much for him. He is unable to complete the ritual, and Huitzilin destroys the Codex and feeds upon the Doctor, leeching out the last of his life and becoming fully corporeal. Which is when Cristian, forgotten in the struggle, grabs Anna’s gun and shoots Huitzilin in the chest, killing him and restoring the Doctor to life.

The Doctor is too weak and Cristian too traumatised to get back to the TARDIS, but Huitzilin’s death has freed Ace, and she and Benny emerge from the TARDIS and search the sinking liner for their companions. Benny finds them both and gets them back to the TARDIS, and on his way through steerage Cristian rescues a baby who would otherwise have died. Ace is lost overboard as the Titanic sinks out from beneath her, but the TARDIS materialises around her, saving her life. The Doctor takes Cristian back to 1980, where Cristian decides to adopt the boy and name him Benjamin, after Benny. Free of the Blue at last, he will be able to make something of his life, and is no longer doomed to die in a worthless gesture in 1994 when he gets in the way of something more powerful than him. But the adventure has left other scars, as the Doctor fears that he is responsible for turning Ace into a killer, the fragile trust between them has been shattered, and Benny is no longer sure whether she wants to travel with them. And elsewhere, their time-altering enemy is preparing to strike again…