Following from the previous episode "TARDIS", the Doctor and Amy had come under attack by a giant shark-like creature which battered the outside of the transparent conduits that link sections of the undersea base. They were forced to escape and are left with no option but to move on, as their way back to the TARDIS had been destroyed by the massive jaws of the monster. As they traversed the tunnels, they were stalked by the beast which is trying to break through.
Arriving at the main building, Amy and the Doctor found one of the base's personnel, Martin Flanagan. Unfortunately, he was trapped in the area because a sentient computer named Jones would not let him in due to the quarantine. The Doctor managed to convince Jones to let them pass through a compromise after giving it recognition for its hard work (something Jones wished for).
Inside Poseidon 8, they met Oswald Fox and Dana Tanaka, who begun to explain the situation. The lights go out, and when Oswald and Dana begun to panic, the Doctor realises there is something else attacking Poseidon 8: the Vashta Nerada. When the lights came back on, to the horror of his coworkers, Martin is found to be dead. nothing left of him but his diving suit and bones.
The Doctor and Amy decide to go fix the generators so that they may keep the Vashta Nerada at bay, all the while avoiding the shark-like Zaralok that continued to stalk them. They arrived to the generator and were faced with two dead divers reanimated by the Vashta Nerada. They avoided them and the generator was turned back on, expelling the Vashta Nerada from the two bodies when light was restored. The Doctor took an environment status chip from one of the divers' suits to have Jones analyse it.
Jones detected that radiation was recorded in the status chip, but was unable to identify what kind it is as it had not records of such radiation. The Doctor deduced was because it was Vortron radiation, a type of radiation caused by rifts in time that as not ordinarily found on Earth. Deciding to focus on curing the disease caused by the radiation, the Doctor asked Oswald to give them the access codes to allow them to find the ingredients he needed to create a cure.
Cracking under the stress of the situation, Oswald forbid the Doctor and Amy from doing so due to the danger posed by the Vashta Nerada. He planed to send the crew up to the surface in escape pods. However, this is actualy a bad idea: if the survivors are not destroyed by the Zaralok, they'll be fish in barrels for the Vashta Nerada.
The Doctor and Amy convince Dana to give them the codes, letting them out into the corridors to find ingredients. Finding a series of vegetables recently harvested in the corridors, the Doctor concocted an antidote and gave one of the serums to Dana. Dana revealed another piece of information: all the strange occurrences started with a mysterious flash of light.
This lead the Doctor to scan the area around the base for the source of these events. The base's scanners revealed a nearby shipwreck, but it was no ordinary shipwreck. It was the wreck of famed US supply ship, the USS Eldridge, which was part of a project to make it invisible. The Time Lords attempted to stop the project, but failed when the ship fell through a dimensional wormhole. However, this project caused the ship to bend the laws of physics and travel through time, the elecromagnetic generator acting then as a gateway through time and space that brought both the Shark and the Vashta Nerada to Poseidon 8.
The Doctor also found that there was an underground tunnel back to the TARDIS and prepared to leave with Amy and Dana to the Eldridge. However, Oswald entered, threatening the Doctor and Amy with a harpoon gun. He ties them up and left to launch the escapes pods with Dana. Using an escape trick he learned from Houdini, the Doctor got untied and unties Amy. They used the secret passage and get back to the TARDIS.The Doctor piloted the TARDIS to the USS Eldridge and told Amy they had to find the controls for the gateway and deactivate them as it was the only way to remove the Vashta Nerada and Zaralok from Poseidon 8 and return them to their own places in time. However, it was easier said than done as Vashta Nerada were on the Eldridge as well, animating the suits of the deceased crew to go after them again. Too make matters worse, the giant shark had found them and was still trying to find a way in to eat them. Making their way through the ship, the Doctor and Amy outsmart most of the Vashta Nerada by luring them into chambers and flushing them away using the water system. Upon reaching the controls for the gateway, the Doctor and Amy find the room is full of half broken machinery due to the ship's rough trip through time; electrical discharges make getting to the controls harder. Managing to navigate their way through a safe path, the Doctor and Amy reach the controls for the gateway. Undoing the damage the gateway has caused was then a race against time; the Zaralok ing repeatedly against the glass to break into the ship for a meal. However, Amy and the Doctor throw the switches for the gateway, sending the shark back to whence it came along with the Vashta Nerada, also ending the radiation.
Back on Poseidon 8, Dana and Oswald are thankful for their help, with Oswald apologising for his actions and offering to let the Doctor and Amy join their Christmas feast of sea pumpkins. However, the Doctor and Amy are more than a little unwilling and secretly enter the TARDIS when Dana and Oswald have their backs turned. The sound of the TARDIS dematerializing makes Oswald and Dana turn around, much to their shock to see their saviors taking off.