Teenager Marc Marshall is sent to Smallmarshes to stay with his aunt while his MP father entertains his constituents. Feeling abandoned and bored, one day he sets off to investigate movement near an empty cottage on the cliffs. A local policewoman, Barbara Redworth, eventually spots Marcís empty backpack on the path leading to the cottage, and investigates... and when she fails to report in, a search party sent out to look for her finds her huddled in a corner of the cottage, in a state of shock, and drawing cave paintings on the walls. A report is sent to UNIT, but when it arrives the Brigadier is in a budget meeting with General Scobie and Sir John Sudbury of C-19, and it is thus the Doctor who first receives the report and realises that another colony of Silurians has woken. Determined to contact them peacefully, he swears Liz to secrecy and sets off for Smallmarshes on his own. His UNIT pass gets him an explanation from police sergeant Robert Lines, but Lines will not show the Doctor to the cottage until morning. Impatient, the Doctor goes alone that night, and while searching the house he locates a secret passage dating back to the smuggling era. He follows the tunnel to the beach, where two Silurians are preparing to depart with the terrified Marc. The Doctor tries to make peaceful contact, but they stun him with their third eyes and take him with them.
The Brigadier is unable to tell his wife Fiona the true nature of his work with UNIT, and he is all too aware that she is growing ever more angry at his unexplained absences and that he has been neglecting both her and their daughter Kate. He plans to take Fiona out to dinner and try to make things up to her, but events and people are both conspiring against him. His old nemesis Sir Marmaduke Harrington-Smythe, whose military career came to a standstill when a young Lethbridge-Stewart exposed his incompetence during a training exercise, has since used political connections to become the director of the Glasshouse, a private hospital for the treatment of soldiers who have suffered major traumas in the course of duty. In this position, he has amassed a great deal of classified information on UNIT operations, and as soon as he has enough proof, he intends to go public with it, breaking the UNIT conspiracy and ruining Lethbridge-Stewartís reputation. To this end, he orders his two most trusted employees, Irish twins Ciara and Cellian, to kidnap WPC Redworth from hospital and bring her to the Glasshouse, where she will be interrogated by specialists in an attempt to find out how to capture a living Silurian.
Liz Shaw has been reconsidering her involvement with UNIT when she receives a phone call from an anonymous stranger, who warns her that there is a conspiracy against UNIT in the highest levels of C-19. Shortly afterwards, someone attempts to assassinate Sir John Sudbury; the assassin fails, but is given a new assignment by his employer, a pale young man with superhuman strength. The raid on the hospital where Redworth is being treated also goes wrong when a woman posing as an investigative reporter apparently stumbles across the kidnapping attempt and kills one of the raiders while escaping. The Brigadierís dinner with Fiona is interrupted by a call from UNIT about the incidents; the bullets at both scenes are government issue, and the dead woman at the hospital has been identified as a Glasshouse employee. He also learns at this point about the earlier report of a possible Silurian incursion in Smallmarshes, where further reports are coming in of mysterious underwater activity. The Brigadier has no choice but to return to duty, and the furious Fiona returns home, takes Kate to her parentsí, and initiates divorce proceedings against him.
The Doctor has been captured by Silurians from a shelter populated by hybrids, who have been ostracised by their pureblood cousins since before the great hibernation. The shelter is led by the moderate Chukk, who barely manages to keep in check his mate Auggi, an extremist who loathes the thought of a world run by mammals and seeks their utter extermination. Chukk questions the Doctor and presents him to the Silurian Triad for inspection; the Triad have woken in a distant shelter and have been observing mankind, while planning how best to go about reclaiming their lost world. Impressed by the Doctorís intelligence and his passion for peace and justice, Chukk explains that his peopleís nature as hybrids of Silurians and Sea-Devil Warriors has rendered them sterile and dramatically reduced their life span. Marc has been kidnapped as a specimen for experimentation; the scientist Baal intends to split apart and analyse Marcís DNA in the hope of finding a cure for their condition. The Doctor is horrified to learn that Marc is already near death, and that the Siluriansí medical equipment cannot heal the damage they have caused, but when he insists upon taking Marc back to the mainland for treatment, Baalís associate Tahni stuns him again to prevent him from interfering with the experiments.
All evidence seems to indicate that the employees of the Glasshouse have been plotting against C-19, and Sir Marmaduke is thus dismissed from his position and bought out to avoid a scandal. He believes that he is once again the victim of a conspiracy to ruin him -- and this time heís right. His enemy is not Lethbridge-Stewart, however, but the pale man, a former employee of International Electromatics who acquired a cybernetic body in the Cybermenís early experiments upon the human form. He has been infiltrating his own people into the Glasshouse for some time now, including the Irish Twins. He now kidnaps Sir Marmaduke to question him about classified UNIT operations, while his assassin kills the scientists in the Glasshouse and kidnaps Redworth. Sir Marmaduke is stunned to realise that the pale man has been behind C-19 every step of the way, cleaning up the mess left behind by alien invaders and collecting a vast Vault full of discarded alien technology with which he intends to rule the world. Realising that he has been played for a fool, Sir Marmaduke stands up to the pale manís torture and dies without breaking. Meanwhile, Ciara and Cellian, still seeking a living Silurian, pose as police to question Marcís parents and then kill them, eliminating all traces of their inquiries behind them.
Lizís anonymous informant places her in touch with investigative journalist Jana Kristan, who has also been alerted to the C-19 conspiracy. Their contact is murdered before he can give them any more useful information, but Jana has unearthed a lead of her own, and Liz agrees to help her investigate mysterious deaths on the Channel Island of LíIthe. Liz and Jana rent a boat and cross to LíIthe, where they find a hidden entrance to the Silurian shelter where the Doctor and Marc are being held. There, the Doctor is being questioned by the hostile council, but just as it seems heís making headway Liz and Jana arrive -- and Jana is revealed to be another of the pale manís assassins, who killed the real Jana and took her place. She came to LíIthe hoping to find a live Silurian but isnít prepared for the numbers she encounters -- and when Chukk confronts her, she shoots him dead, and also shoots Liz when she tries to run. The Silurians kill Jana, and the Doctor puts Liz into a trance to slow her metabolism and give her body a chance to heal. But Auggi is now the leader of the shelter, and the Doctorís hope for peace has been lost.
While the Brigadier and a squad of UNIT soldiers search Smallmarshes for some sign of the Doctor or the suspected Silurian incursion, Benton and another team are sent to the Glasshouse to remove classified materials pending Sudburyís investigation; however, they find that someone else has beaten them to it. Meanwhile, Sergeant Mike Yates is in just the right position to see a stealth plane landing in Smallmarshes, bringing a team from the Vault, and he knocks out one of the newcomers and takes his place, intending to investigate further.
Baal completes his research and allows the Doctor to depart with the grievously genetically wounded Marc. He has no objection to allowing the Doctor to try to cure him, and wants to get him out of the way before Auggi learns that he has been considering augmenting their DNA with that of ape-primitives. Tahni pilots the Doctor and Marc back to shore, but Auggi detects their departure, concludes that Tahni has betrayed her and has the submersible destroyed. She also detects the military presence in Smallmarshes, and leads a squadron of warriors to the mainland, intending to show her superiority by wiping out the Ape forces. Baal, realising that Auggi is beyond reason, returns to the laboratory, where the recovering Liz surprises him and his assistant Sula by correctly identifying much of their equipment and deducing from first principles what it is they are doing. Baal and Sula put aside their prejudices and allow Liz to assist them, and finally realise that it is possible for their kind and humans to work together. Meanwhile, despite attacking the UNIT troops with all of the weapons at their disposal, including a Myrka, Auggiís forces are overwhelmed and driven back. When she calls back to the shelter for reinforcements, Baal refuses to help her, and the furious Auggi retreats to the Triadís shelter, intending to fight on another day.
The Doctor gets Tahni and Marc to safety before the submersible is destroyed, but they are then captured by the C-19 team and taken to the Vault. There, the Doctor is brought before the pale man, who reveals that he intends to use the alien technology in the Vault to take over the world. He orders the Doctorís guard to take him away for torture and interrogation -- but the guard turns out to be Mike Yates in disguise, and he and the Doctor surprise the pale man and escape. The Doctor tries to rescue Tahni from the interrogation rooms, only to be confronted by the Irish Twins -- who reveal that they have been augmented with Nestene technology and transformed into walking weapons. They accidentally kill WPC Redworth while trying to gun down the Doctor, and before they can kill him Yates opens the gates of the Vault, letting in a UNIT team who had tracked the transponder codes of the stolen stealth plane. The pale man and the Irish Twins flee to fight another day, but the strain has been too much for Marc, whose heart has given out from shock. In the aftermath, the Brigadier arranges for Baal and Tahniís shelter to be left in peace, and Mike Yates is promoted to Captain -- but Liz has had enough. She tenders her resignation from UNIT, planning to return to Cambridge and continue her researches, and hoping that she will be able to make a difference to the world with what she has learned from the Doctor.