The Doctor and Amy are inside the TARDIS, discussing where they should go next for a more peaceful outing, which is nearly impossible considering the Doctor's long track record of vacations failing miserably. However, the TARDIS suddenly enters a 'space riptide', and the Doctor is launched through the doors and out into space. After the TARDIS steadies itself, Amy looks outside and sees the Doctor hovering, still conscious and surrounded by a number of strange blue worms, a short distance away.
Through sign language, he managed to tell Amy that he is slowly suffocating, and she can save him by resetting the TARDIS oxygen shield by using the red levers. Amy does so and the Doctor uses an earpiece to properly contact her through the view screen and told her to use the tractor beam to pull him back in. However, the console would need an outside power source for that and he sent Amy to his drawing room to retrieve something to power the beam. Searching through the many nick-nacks in the Doctor's drawing room, Amy is at first unsuccessful in finding anything useful for powering the tractor beam. Another riptide occured and one of the clocks on the moves to reveal its the door to a safe. Amy found the Master's Laser screwdriver inside, but accidentally knocked over a vase next to it. Thinking she can just replace it, Amy hurries back to the control room. Unbeknownst to her, a orange glow escapes the shattered pieces of vase and follows after her. After informing the Doctor through the veiw screen that she found the laser screwdriver, the Doctor instructed her to insert it in the console. Doing so activates the tractor beam and the Doctor is pulled back into the TARDIS.
The Doctor explained that the blue worms that had been pestering him are known as Chronomites, somewhat harmless parasites, but they can make you 'very itchy'. Unfortunately, the Entity, a old enemy of the Doctor that survives by draining years from others, had arrived in the control room. The presence of the Entity, along with another space riptide, causes the TARDIS to send Amy away.
Amy was then in a future TARDIS with the Entity. Realising that Amy is in the TARDIS 1,000 years into the future, the Doctor set about scavenging parts from the present TARDIS in order to create a tachyon feedback loop which will reunite Amy with him. The Doctor managed to scavenge three items from his drawing room; his Fob watch, an Oscillator from the distress beacon he picked up in the GSO Arctic Drilling Station and the Krontos Crystal used to make a chronal blocker on Skaro; using these, the Doctor was able to successfully make the feedback loop.
In the future TARDIS, the Entity begun attacking Amy to suck the time out of her. A time-activated recording of the Doctor contacted Amy and tells her that she needs to answer some trivia in order to prove that she's herself; then she could access and use the tachyon feedback loop to return to her proper timeline. Amy answered the trivia correctly and completes the loop on her end, allowing the Doctor to pull her back into the present TARDIS.
Once reunited, the Doctor threatened the Entity to restore Amy's time or he would re-imprison it after it finishes her off. The Entity retreated into another vase the Doctor took out and is given a deal in return. The Doctor would release the Entity into the timestream, where it can feed off of the limitless supply of Chronomites. The Entity found this to be an acceptable offer and was released from the TARDIS. However, Amy told the Doctor that he forgot to mention that the Chronomites cause itchiness. The Doctor simply sayed he forgot, possible meaning he wished to give the Entity some kind of punishment for it's past deeds.
The Doctor finished some diagnostics with the TARDIS and sets course for Poseidon 8, built in London's previous location following the great flood of the 23rd century. Exiting the TARDIS, Amy was amazed they were at an underwater base. However, her amazement was replaced by fear as both she and the Doctor noticed a gigantic alien shark attacking the base and coming towards them...