Twelve thousand years in the future the Doctor and Amy arrive in a museum where the Doctor apparently is looking for things from his own adventure. He is drawn to the box, now somewhat battered. He tells Amy that it is a Home Box - like a black box flight recorder except it homes - and written on it is a message in the lost language of Time Lords. Amy asks what it says and the Doctor translates "Hello sweetie". The Doctor steals the box and he and run back to the TARDIS, pursued by two guards. .
The Doctor plugs into the box's security feed and sees River Song in front of an airlock. She gives a space-time coordinate. She is confronted by the man and the two guards who ask why she is still there after the party has finished. She tells them that she wanted to see what they had in the ship's hold and adds that the ship will never reach its destination. She then tells them that they may want to hang onto something. The airlock opens and River is ejected into space. The Doctor sets the TARDIS controls for this time and place and arrives beside the ship in time to open the TARDIS doors and let her in. She lands on top of him. While Amy gazes at the pair of them quizzically, River tells the Doctor to "Follow that ship."
The TARDIS chases the Byzantium as it switches to warp drive. The Doctor is manically flicking switches and pulling levers as the TARDIS shakes about violently. River tells him to switch the stabilisers on. He retorts that there are no stabilisers until she flicks some blue switches and the shaking stops. He looks angrily at them and calls them 'blue boringers'. River smoothly takes over the flight and says that she has parked the TARDIS beside the Byzantium. Again, the Doctor argues. He says that they can't have landed because there was no customary wheezing noise. River tells him that the TARDIS isn't supposed to make that noise; it's just that the Doctor leaves the brakes on.
River goes out to see why the Byzantium chose to land here. The Doctor shuts the door behind her and prepares to leave. Amy wants to know who River is and why the Doctor is running away. He says that River is his future and that time is not the boss of him. She pleads to be allowed to go outside because she has never been on an alien planet before. They step outside 'for five minutes' and stand on a beach. Above them, on top of a huge building, the Byzantium is in flames. The Doctor says that, according to the Home Box, there were no survivors and the crash was caused by a phase shift in the warp engines. River says that indicates sabotage. She says that the building is an Aplan temple and has been deserted for centuries.
Amy asks who River is so the Doctor introduces them. He accidentally calls River 'Professor' to which she replies 'spoilers'. She adds that there is one survivor: something in the belly of the ship. She says that it can never die. River calls up soldiers that are in orbit around the planet. Four men dressed in camouflage teleport onto the beach. Their leader, Father Octavian, is impressed to meet the Doctor and says that he has a further twenty men in a drop ship. River asks the Doctor what he knows about Weeping Angels.
The drop ship lands beside the temple and the soldiers - Clerics - emerge to set up camp. Father Octavian says that they cannot enter the ship from above because it is too close to the drives and so they need to blow their way into the cliff face from which the temple is carved and make their way up through the Maze of the Dead. Amy asks if the Doctor is Mister Grump-Face today and he launches a tirade about how he is facing one of the most malevolent creatures in the Universe which he will have to defeat in a way he hasn't yet thought of. He asks her if she has any more questions. When she asks if River is his wife from the future he says "Yes... I am Mister Grumpy-Face today." He tells Amy that the Father is a Bishop in the army. He adds that this is the fifty-first century and the church has moved on.
River calls them into the drop ship where she has a video of the Weeping Angel she ripped from the Byzantium security cameras while she was on board. The tape is on a four second loop. The Doctor and River explain to Amy about Weeping Angels. The Doctor says that the only time he met them before they were scavengers, barely existing. He tells Amy that the Angels can move and this one is not 'dormant' as River suggests, merely patient. The Doctor, River, and Father Octavian leave the drop ship and the Doctor tells them that the radiation from the Byzantium, deadly to almost everyone, is dinner for the angels. Father Octavian tells him that the indigenous people, the Aplans, died out but since then the planet has been Terraformed and is home to six billion humans.
River tells the Doctor that he has given her pictures of all of his faces so that she can recognise him when they meet. She also has a book that explains the Angels. He reads it in seconds and wonders why there are no pictures. He leafs through and finds a passage that says that "anything which holds the image of an angel becomes itself an angel".
Amy looks at the loop of the Angel on the screen and is puzzled to see the Angel has turned to face the camera. Every time she looks away it has moved again: its hands drop from its eyes, it gets closer and, finally, it leaves the screen and comes into the room. She tries to use the remote to turn off the screen but it keeps on switching back on. The door of the ship is locked, too. The Doctor and River become aware of her predicament and try to get in but can't. The Doctor shouts at Amy to keep looking at the Angel but not its eyes for they are "not the windows of the soul but the doors. Beware what may enter there." Amy freezes the loop at the split second where there is only image noise. The drop ship door opens and the Doctor and River enter. River congratulates Amy on her success but Amy has something in her eye.
The Clerics blast a hole into the Maze of the Dead and enter. The Doctor uses one of their gravity globes to light up the chamber where they see that the walls and paths are lined with stone statues. Octavian orders his men to make a visual inspection of each in order to find the Weeping Angel. He then pulls River to one side and says that the Doctor doesn't know who she is yet. She says that it is too early in his time stream but she has no intention of going back to prison.
Amy rubs her eye again and dust runs out through her fingers. Clerics Christian and Angelo explore a smaller chamber. They separate and Christian's rifle's light flickers. He sees a Weeping Angel about to attack. Christian calls for Angelo to come and see something. He too is attacked.
Cleric Bob panics and shoots a statue. Octavian tells the Doctor that the Clerics' names are sacred: given to them when they enter the service of the church. Octavian sends Bob back to guard the entrance Christian and Angelo.
The Doctor, Amy, River, Octavian, and the other Cleric soldiers climb up the paths of the chamber. River and the Doctor are discussing the fact that the Aplans had two heads when they realise that all of the statues have only one head. The Doctor orders everyone to turns off their torches for a split second. When they switch them back on they see that all of the statues are climbing towards them: they are all Weeping Angels. The Doctor thinks that they have been without food for centuries and are degraded but the Byzantium was crashed here deliberately to feed them with radiation.
Angelo calls Cleric Bob gets to come and see something. Bob is attacked by the Weeping Angel from the ship. Octavian calls Bob to tell him that all of the statues are Angels. Bob replies that he knows and that he is dead: his neck was snapped and the Angel took his cerebral cortex so that it could have a voice. It has reanimated a version of his consciousness so that it can speak to them. Bob adds that the Angel is on its way up.
The group runs towards the wreck of the Byzantium. Amy cannot run because she thinks her hand has turned to stone and is gripping a rail, trapping her. The Doctor tells Amy that she has looked into the eyes of an Angel and it is playing with her mind. The Doctor bites Amy's hand and the two run on. She complains about being bitten by "space teeth".
The remaining members of the party find themselves beneath the Byzantium but it is too high to reach. Bob calls again with a message for the Doctor: the Angels are "very keen" that he knows Bob died afraid and in pain. River realises that the Angels are trying to make the Doctor angry. Octavian details his men to guard the entrances to this chamber and they report Angels arriving in every passage. The Doctor says that the Angels have made a mistake. He asks if the survivors trust him and then asks for Octavian's gun. He tells everyone to jump when he does something extremely "stupid and dangerous". Bob calls to ask what the mistake was that the Angels made. The Doctor responds: "There's one thing you never want to put in a trap. If you're smart, if you value your continued existence, if you have any plans of seeing tomorrow then there's one thing that you should never, put in a trap...... Me." He shoots up at the gravity globe.