In a parallel universe, the Neptune was the submarine the smuggler Hoskins used for his business. He took the Doctor and Ruth Mills (who had stowed onboard inside a compartment used for smuggling, which surprised and angered both Hoskins and the Doctor, particularly surprising Hoskins since the compartment was meant to be hidden) down to the DEEP.
The Doctor had brought onboard the sub equipment to jam military sensor probes to allow them to reach the DEEP without being detected. The sub was damaged in the attempt and was abandoned when its owner was killed by General Flint who had survived for 27 years, and Ruth used an escape pod to reach the surface instead.
Ruth mocked the Neptune when Hoskins claimed it was the fastest mini-sub around, asking if it should have been named "the Titanic" instead. (AUDIO: Full Fathom Five)