This is the second part of a two parter episode. The Doctor has discovered that Silurians living in a sleeping state under a welsh village are now waking up. He has lost Amy Pond who has fallen through the ground.
The Doctor is underground with Nasreen, lead geologist and have discovered a large number of Silurians in deep sleep. Some Silurians who belong to the military are now awake and have now captured the Doctor and Nasreen. The Doctor and Nasreen are taken to the Silurians medical doctor. When the Medical Doctor discovers that the Doctor is not human, Restac, the military leader takes them to the execution chamber to be shot. Before the execution is about to be carried out, Amy Pond arrives with Ambrose's husband and attempts a rescue which fails. Amy and Mr. Ambrose are tied up along with the Doctor.
The Silurians make contact with Rory Williams and tell him that they need to bring Alaya down or they will execute the prisoners. The Doctor is unaware that Alaya was killed by electrocuted by Ambrose when Alaya became aggressive and uncooperative. Rory decides to still go down with two members of the group and the body of Alaya.
When Rory comes down, he has the body of Alaya and lays it out. When Restec sees that Alaya who is her sister is dead, she attempts to carry out the execution but the Doctor uses his sonic screwdriver to disable the Silurians weapons. The leader of the Silurians, Eldane has a plan to resolve the situation. He plans to flood the caves with poisonous gas forcing the Siluarians to get back into their sleep chambers for another 1000 years but which time, the humans above ground should be ready for them.
Everyone heads to the TARDIS for evacuation. When they reach the TARDIS, the Crack in the universe is spotted on the cave wall, the Doctor puts his arm through and grabs something but doesn't look at it. Restec arrives and shoots but hits a heroic Rory Williams instead of the Doctor killing him. Light streams from the Crack in the Universe come out and touch Rory thus erasing him from history. Amy Pond is inconsolable but after they return to the ground, all memory of Rory has gone. The Doctor looks at the object he retrieved from the Crack and it turns out to be piece from the TARDIS.