Deep-sea Energy Exploration Project

In a parallel universe, the Deep-sea Energy Exploration Project was a scientific/military base manned by Professor Eric Vollmer and his assistant Lee.

History
Vollmer was a scientist interested in renewable energy sources, but was completely unaware that the military who had funded his work didn't care about his work on using harnessing the hydrothermal vents on the sea floor though General Flint kept up the pretense for appearances when he visited the base.

In truth Flint was more interested in Lee's work in genetic experiments which had been banned by numerous international treaties. Lee had used stem-cells from the unique marine life and injected them into human clones grown in his laboratory. Flint wanted a "future" of genetically-enhanced super soldiers and funded Vollmer's own research without the scientist realising the truth.

When the Doctor arrived, Flint had Lee inject Vollmer with the enhanced DNA while he primed the base's self-destruct system, linked to six bombs outside the base, determined not to leave any loose ends. The explosion would have contaminated the sea floor for miles around.

Flint was injured when the infected Vollmer tore off his arm and the countdown began, and Flint began to transform himself, and the Doctor was forced to escape in an escape pod, but not before he shot Vollmer, an act witnessed by Flint on the security cameras.

The Doctor escaped, leaving his TARDIS behind in what he assumed was an explosion that destroyed the base. But Flint and the base survived by shutting down the self-destruct sequence though he couldn't turn off the dirty bombs outside the base, saturating the water with radiation - he knew the Doctor would return someday and planned to wait for him to return for his ship.

27 years later, the Doctor returned, accompanied by Hoskins and Ruth Mills, Vollmer's daughter. While the Doctor was preoccupied with destroying Lee's work, Hoskins downloaded the security footage from the computer. Flint killed him and confronted the Doctor and Ruth, making her learn what happened to her father. (AUDIO: Full Fathom Five)