Parallel universe (Full Fathom Five)
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There existed a parallel universe, in which one version of the Doctor believed the ends justified the means, and he was willing to go to any means to ensure that they were reached, even deception and murder.
In 2039, scientist Eric Vollmer was conducting research into supplying mankind with new energy resources, but the military led by General Flint deceived him by supplying him with a research base known as the Deep-sea Energy Exploration Project so he could have access to "the black smokers," chimney-like structures on the seabed where the superheated water could provide electricity.
In truth, Flint and the military used the DEEP to hide Lee, a discredited geneticist who was conducting illegal and unethical experiments using human clones to create new supersoldiers with the unique marine life nearby.
The Doctor somehow learnt of the project conducted by Lee and Flint and sought to stop it. He reached out and contacted Vollmer, deceiving him into giving him information before Flint arrived at the DEEP to inspect the results of Lee's experiments. Vollmer discovered what Lee was doing, and when the Doctor arrived at the base Flint became suspicious. He already had his superiors guessing what was really going on and he needed to destroy the base to cover his tracks while taking the results with him.
When the base was set to self-destruct, Lee had already injected Vollmer, an unwilling test-subject, with his DNA mutagen and he transformed painfully into a mutant. The Doctor killed Lee after the scientist tried to justify his work, even comparing it to the Nazis and their atrocities since the medical data gathered later went on to save lives.
Flint was also infected by the mutagen when Vollmer attacked him and tore off his arm, and he began to transform. Flint had taken the key to the Doctor's TARDIS, and refused to give it back. With the self-destruct armed and with no time to really search for it, the Doctor had to escape in a submersible. Along the way he encountered the mutilated Vollmer, who pleaded with him to help cure his condition. The Doctor pretended to accept, but shot Vollmer and escaped. (AUDIO: Full Fathom Five)
A year after the Doctor lost his TARDIS, he tried to get it back. (PROSE: Sustainable Energy)
27 years after the DEEP was supposed to be destroyed, the Doctor learnt through covert means the base was actually intact and the military were going to go to recover all research data relating to Lee's work and then destroy it.
During the time gap, Vollmer had been vilified and was used as a scapegoat for the radioactive contamination which resulted in the loss of many businesses, including Hoskins's father. Ruth, Vollmer's daughter, and her mother paid for this blame, and they had to change the family name to escape the grief.
The Doctor had been taking care of Ruth for 27 years, helping her, but when the opportunity came for her to learn more about what had happened to her father the Doctor refused to let her come down. He cited it was because of the danger, but in truth he didn't want her to come down because he would have to kill her to prevent knowledge of Lee's work spreading. But Ruth stowed away onboard the Neptune, Hoskins' submersible to venture down into the DEEP. When they were down there, Ruth learnt the truth of what had happened and that the Doctor had always known the truth of what had happened. Hoskins was killed by Flint, who had also survived the radioactive contamination. The Doctor destroyed Lee's remaining notes so no-one could find them.
Flint, terribly mutated, confronted the Doctor and Ruth, and Ruth learnt the Doctor had shot her father and learnt the Doctor's real motives for going to the DEEP were not for her, but to destroy Lee's work and to destroy the DEEP once and for all while recovering his TARDIS key. Flint showed the key and shoved it down the Doctor's throat, snapping it. Ruth watched on angrily but she held onto Hoskin's gun ready to kill the Doctor after he'd told her about his power to regenerate. When the regeneration occurred, the new Doctor barely had time to say "Hello, I'm the Doctor. Who are you?"
Coldly Ruth shot the new Doctor, ready to kill all of the remaining lives the Doctor had to see him dead once and for all. (AUDIO: Full Fathom Five)
