For 27 years, the Doctor has been Ruth Mills’ surrogate father figure, but now they’re having the biggest argument of Ruth’s life. Somehow, the Doctor has acquired a top-secret report and learned that an unmanned military probe has found the DEEP naval base intact on the sea bed, though it is still heavily contaminated by radioactive fallout. Tomorrow, a manned mission will enter the DEEP to salvage the research data believed lost years ago, but the Doctor is determined to get there first. He has hired the submariner Hoskins to take him there, bribing him well in order to convince him to break the military quarantines. However, Ruth has caught sight of the report as well and insists upon accompanying the Doctor to find out what really happened to her father. The Doctor refuses, claiming that it’s too dangerous; he promised her father that he’d keep Ruth safe, and he intends to keep that promise. Ruth’s frustration grows when Hoskins heaps scorn upon her father; for years, people have believed that Eric Vollmer was responsible for the disaster which poisoned the fish stocks for miles around, and her mother never really recovered, even after changing their family name. The Doctor promises to return with the answers Ruth wants, but flatly refuses to let her accompany him. Realising that she can’t talk him around, Ruth sadly bids him goodbye, and the Doctor, satisfied, helps Hoskins to load some specialised equipment onto his mini-sub, the Neptune.

27 years earlier: Professor Eric Vollmer is contacted by Dr. John Smith, who claims to have learned of his work through a mutual colleague. Though the work is classified, Smith has credentials with UNIT and Vollmer is happy to share his findings with a fellow scientist. Vollmer is studying the possibility of using black smokers, hydrothermal vents on the sea bed, as renewable energy sources, and although all of his test turbines have melted in the heat he remians optimistic. However, he is somewhat irritated that his assistant Lee is spending more time on his own side-projects than helping him. Dr. Smith also seems interested in Lee’s work, and Vollmer admits candidly that he’s becoming concerned; Lee’s experiments involve genetic engineering for military purposes, and lately he’s refused to discuss his work with Vollmer. Nevertheless, their military liaison, General Gordon Flint, will arrive tomorrow to inspect Vollmer’s work, and Vollmer is looking forward to making his presentation.

The Neptune approaches the DEEP, and the equipment which the Doctor installed generates a counter-signal fooling the quarantine mines into believing that the mini-sub is organic. But the Doctor’s plan goes awry when Ruth emerges from hiding, having stowed away while the Doctor was helping Hoskins earlier. The Doctor is enraged, but the Neptune doesn’t have enough fuel to return her to the surface and get back down to the DEEP before the military arrives, and the Doctor thus has no choice but to press on. The DEEP eventually comes into view, all but shielded by the upflow from the black smokers created when the explosions 27 years ago tore open the sea bed. The heat from the black smokers nearly melts the hull as Hoskins moves in, but the Neptune makes it through safely and prepares to dock with the DEEP.

General Flint arrives at the DEEP, cuts through Vollmer’s initial pleasantries and insists upon starting the inspection at once. He rushes Vollmer’s presentation on to the bottom line, and Vollmer admits that full-scale exploitation of the black smokers won’t be possible for another 30 or 40 years. Vollmer is puzzled by Flint’s amused reaction, even more so when Flint demands to see Lee’s experiments. But when he finally learns what Lee has been doing under his nose, he’s sickened. He had trusted Lee absolutely, and Lee has repaid him by diverting funds to create genetic abominations which he refers to as “works in progress”. Lee accuses Vollmer of jealousy that his assistant has outdone him, and Vollmer in turn accuses Lee of abandoning scientific ethics in search of a non-existent quick fix. But the final word goes to Flint, who reveals that he never had any interest in the black smokers. Vollmer was hired to act as the public face of the DEEP because he was gullible enough not to notice what was really going on down here...

While Hoskins checks over the damage to the Neptune, the Doctor sets off to explore, reluctantly allowing Ruth to come with him and assuring her that if the Neptune really is damaged beyond repair then they can leave in the DEEP’s one remaining mini-sub. At least, two of them can... The Doctor and Ruth soon find Vollmer’s lab, which appears to have been trashed by someone searching for something. Hoskins then calls to report that he’s going to have to search for parts to repair the Neptune, and the Doctor, suspicious, leaves Ruth to search her father’s lab while he confronts Hoskins. He finds the puzzled Hoskins staring at an anachronistic police box he’s found in another lab, and warns him that he knows Hoskins had ulterior motives for accepting the Doctor’s bribes. He suspects that someone else is paying Hoskins as well, to learn the truth about the DEEP -- but the Doctor is here to ensure that nothing leaves the DEEP, and he warns Hoskins that he’s willing to do whatever it takes.

Vollmer has always worked for the long-term benefit of mankind, and he still can’t quite grasp that Flint and Lee really are only concerned with short-term goals. Lee reveals that he’s ready to test his work on a natural-born adult human rather than the clones he’s been using until now, but as Vollmer protests this grotesque breach of scientific ethics, a strange wheezing, groaning sound comes from the nearby laboratory. Flint sends Lee to investigate while he spells out some home truths for Vollmer, but Lee returns with a stranger who, to Vollmer’s surprise, identifies himself as Doctor John Smith...

Ruth goes out looking for the Doctor when he fails to return, and is shocked to find him in another lab, tearing up and burning the notes he’s found there. The laboratory is lined with tanks containing partly rotted bodies, all disfigured and mutated. The Doctor reveals that Ruth’s father’s assistant was conducting illegal experiments to create super-soldiers with the characteristics of marine predators, and that Ruth’s father was only ever meant to serve as a smokescreen and a scapegoat. But now the Doctor is destroying the evidence that could clear Vollmer’s name, and he’s forced to admit the truth to Ruth at last. He’s always known what happened to her father, and he didn’t come here to uncover the truth -- he came here to ensure that it stays buried forever.

Flint questions the Doctor and confiscates the key to the blue box which Lee saw him emerge from. The Doctor refuses to explain how he penetrated this secure military facility, but does admit that he lied to Vollmer in order to find out what Lee was up to. He has no qualms about abusing Vollmer’s trust, since the scientist had been turning a blind eye to his assistant’s illegal work. Though Lee is holding him at gunpoint, the Doctor is confident that the nervous young man isn’t quite ready to commit his first murder, and that Flint won’t kill him until he learns who the Doctor is working for and how he penetrated the DEEP. Flint tries to beat the truth out of him, but the infuriated Vollmer intervenes, refusing to be a party to torture and vowing to reveal everything he’s learned today. However, his naïvete has led him to make a grave error, for Flint concludes that Vollmer has intervened on the Doctor’s behalf because they are working together, and by threatening to reveal classified information Vollmer has just committed treason. This is punishable by death, and Lee needs an adult human to conduct the next stage of his experiments...

As Ruth tries to absorb the Doctor’s revelation, Hoskins calls them in a panic -- but all they hear is screaming, snarling and gunfire. When they investigate, they find that Hoskins has been torn apart by something which aparently emerged from the underwater dock. Though shocked by Hoskins’ brutal death -- and by the Doctor’s casual, analytical attitude towards it -- Ruth takes Hoskins’ gun for protection and follows the Doctor away, still demanding to know what really happened here 27 years ago.

Flint takes a syringe full of Lee’s enhanced DNA formula and places it to Vollmer’s neck, demanding that the Doctor answer his questions. The Doctor refuses to do so, but Flint isn’t bluffing, and he injects Vollmer with the syringe’s contents. As Vollmer begins to convulse, Flint orders Lee to keep the Doctor covered and monitor the changes to Vollmer. Flint himself leaves to prepare for his departure. The Doctor helps Lee to restrain Vollmer, and Lee admits that he mixed the genetic cocktail with growth-enhancement drugs, cutting corners so that he’d have something to show Flint when he arrived. Vollmer’s entire body is changing, and before losing consciousness, he begs the Doctor to kill him. Meanwhile, Flint activates the DEEP’s self-destruct facility, links the bomb to six other devices planted outside, and downloads the initiation sequence to his personal palm-pad unit. He will leave no loose ends behind...

The Doctor burns the last of Lee’s notes while Ruth tries to come to grips with learning that the Doctor, a man she’s known and loved all her life, has been lying to her all that time. The Doctor then demands that Ruth get to safety in the escape pod before whatever killed Hoskins tracks them down, promising to follow in the Neptune once he’s finished his work here. Ruth refuses to leave until the Doctor has confessed everything, and the frustrated Doctor agrees to tell her the whole story on the way to the escape pod.

Vollmer passes out, leaving only the Doctor and Lee to debate Lee’s ethics or lack thereof. Though clearly uncomfortable about what’s happened, Lee defends himself by pointing out that great scientific progress is made in times of war and that the data collected by Nazi doctors has been used to save lives. But he still can’t bring himself to shoot the Doctor, even when the Doctor approaches him and wrestles the gun away from him. It’s time for Lee to face the consequences of his actions, for the Doctor knows that his experiments could lead to the end of the world. What if the Doctor believed the ends justified the means? What if he was willing to take the cheap, easy solution? Lee, terrified, begs for his life... but the Doctor shoots and kills him.

Ruth is stunned by the Doctor’s casual confession and his complete lack of remorse. He claims that killing Lee was the only way to ensure that his experiments never saw the light of day, and that some things are more important that individual human lives. Ruth realises that she’s never really known the Doctor at all... and now that she knows the truth about what happened here, what will the Doctor do to stop her from telling it?

Vollmer revives, shaken but alive; however, the mutation is continuing, and, aware that he’s unlikely to survive much longer, he begs the Doctor to take care of his daughter. The Doctor reluctantly promises to do so. Flint then arrives, and is surprised to find that the man he’d dismissed as a bleeding-heart liberal has just murdered Lee is cold blood. However, Flint has prepared for this moment; his own superiors were unaware of what Flint was funding here, and he intends to destroy all evidence of his work behind him. When he triggers the DEEP’s self-destruct sequence, six dirty bombs will tear apart the sea bed and contaminate the entire area with lethal amounts of radiation, covering Flint’s tracks while he takes Lee’s notes away so others can restart the experiments elsewhere. Before the Doctor can stop him, the enraged Vollmer attacks Flint, tearing off his arm -- and as Flint drops his palm unit, the countdown begins. When Flint regains consciousness, he finds that Vollmer has gone and that the Doctor has tied off the stump of his arm with a tourniquet; however, he knows that the Doctor didn’t do so out of kindness, and the Doctor admits that he needs Flint to tell him where he’s hidden the key to the TARDIS. Flint refuses to do so, and with no time to search the entire base, the Doctor leaves Flint to die and heads for the escape pods.

Before the Doctor and Ruth reach the escape pod, they are confronted by the thing which killed Hoskins, something which has been waiting for the Doctor to return for 27 years. Despite the Doctor’s warnings, Ruth pushes past him to speak to the monster she believes is her father -- but when it steps out of the shadows, she faints from sheer terror, and only the Doctor is left to greet the thing that was once General Flint. When Vollmer attacked Flint 27 years ago he infected Flint with the enhanced DNA, and when the Doctor left him for dead, Flint deactivated the self-destruct sequence, knowing that the Doctor would one day return for his blue box. However, he was unable to deactivate the dirty bombs, and the escaping Doctor assumed that the DEEP had been destroyed in the ensuing explosion. For 27 years, the base has been cut off from the outside world by the radioactive fallout, and Flint has been here alone, waiting for the Doctor to return. Ruth awakens, still shocked but pulling herself together, and Flint demands that the Doctor tell her the last secret of the DEEP -- the truth about her father’s death.

With only two minutes to go before the DEEP is destroyed, the Doctor reaches the escape pods -- only to find Vollmer waiting. The mutation has stabilised, and Vollmer believes there’s a chance to reverse it. He no longer wants to die, not while there’s a chance to put this right, and he begs the Doctor, as a fellow scientist, to work with him. The Doctor reluctantly agrees to do so... but when Vollmer turns to enter the escape pod, the Doctor puts a bullet in his back, and departs from the DEEP alone.

Again, the Doctor claims that his actions were justified; though he did trust Vollmer to keep his change a secret, he simply couldn’t risk the possibility that someone else would find out and resume Lee’s work. Ruth finally understands that the Doctor never came here to “learn the truth” -- he came here to destroy the DEEP and recover his TARDIS, and if he’d succeeded, he would have departed without word, leaving the ignorant Ruth to mourn another loss. The Doctor admits that he always knew he wouldn’t be able to let Hoskins leave here alive -- and though he tried desperately to keep his promise to Vollmer by keeping Ruth away, now she too has learned too much. But Ruth still has Hoskins’ gun. Flint reveals that he still has the TARDIS key, and as Ruth stands by, watching, Flint forces the key into the Doctor’s mouth and snaps his neck when he refuses to swallow it.