The robot tells them that they are in a "kindness facility", dealing with the Chen-7 plague, an illness that only afflicts races with two hearts. This includes the native Apalapucians and, naturally, Time Lords. After delivering its message the white Handbot beams away.
Rory goes back out of the room and tries to re-enter by pressing the red waterfall button but Amy isn't there. The Doctor tells him that it isn't as simple as that and says that he needs to take the glass back to the TARDIS to get a lock on her position and smash through time to get her. He tells her to enter the facility and leave a sign so that he can find her. He warns her to stay away from the Handbots; they won't recognise her as alien and their kindness will kill her.
In the TARDIS, the Doctor fits Rory with a pair of glasses that act as cameras so that the Doctor can follow his actions. He says that if he enters the facility it will be instant death but it will be less dangerous for Rory. Meanwhile, Amy walks through the facility, finding it largely deserted except for the holograms that offer her entertainment opportunities and the Handbots. These try to inject her with medicines. Amy tells them that the medicine will kill her but they reject this statement and pursue her. She leaps down an access passage and tries to hide out underground. The Handbots soon track her down but when she hides in a cage that seems to be connected to a shaft of some sort the robots walk by. Even though she is in plain sight there is something in the vapour emitted from the cage that shields her.
The Doctor has to stay in the TARDIS because of the plague but he takes the ship into the red waterfall time stream and Rory exits. Meanwhile, Amy has passed through a portal into the gardens where she talks to the interface and finds that the Handbots couldn't see her due to the exhaust from the temporal engines. Two Handbots close in on her but she neutralises them by pulling their hands into contact with each other. She then makes her way to the temporal engines, leaving a note on the door of the engine room to tell the Doctor where she is.
Rory explores the facility which is deserted. The Doctor tells Rory to use the sonic screwdriver on the time glass (which he has taken with him) and this allows them to see forty thousand time streams and the Red Waterfall full of people. Rory is attacked by a futuristic Samurai warrior who turns out to be Amy. Unfortunately she has been waiting for 36 years and has grown bitter with hatred for the Doctor. She saves Rory from a Handbot by stabbing it through the face with her word. As she leads Rory through the facility she shuts down two other Handbots with her trick of holding their hands together so they feed back. She says that she has made a sonic probe which manages to convert the Handbots' 'black box' devices to transmit their demise as accidental. She takes Rory to her den where he meets her pet, a Handbot called Rory from which she has removed the hands. She speaks to the Doctor through Rory's glasses, telling him that her life has been hell.
Amy leads the Doctor into the garden where he can use her to speak to the interface about the temporal engines. Rory wanders off alone and is about to be killed by the kindness of one of the Handbots when it is decapitated by Amy. The Doctor says he has worked out how to fold time to get top the younger Amy's time stream but Amy refuses to participate in this. She says that it will mean her death and the younger Amy will replace her. She demands that they take her with them as she is.
Rory blames the Doctor for all of this, telling him to read a history book and find out about outbreaks of the plague. The Doctor retorts that that isn't how he travels. When Rory throws the glasses onto the floor the Doctor detects the younger Amy in the same place, but 36 years earlier. Rory uses the time glass to see her and then to get the older Amy to converse with her younger self. However, the older Amy remembers this conversation from when she was younger and says that the older Amy refused to help and the Doctor and Rory left in the TARDIS. The younger Amy, this time, asks the older Amy to change her mind, to consider Rory in all of this. After discussing why they fell in love with him in the first place, the older Amy decides to help. Her demand is that the Doctor takes her too. The Doctor says this will be extremely difficult but not totally impossible. He says he will have to jettison the karaoke bar to compensate the paradox and suggests that Rory's marriage might suffer by having two Amys aboard.
The Doctor instructs Rory how to reroute the time streams via a control panel while the two Amys synchronise their thoughts. They both think of their first kiss with Rory to the tune of 'The Macarena'. Both Amys appear, face to face. This causes the glasses to short out, leaving the Doctor out of touch. The TARDIS starts to go into launch procedures to get away from the paradox. The Doctor realises that they have eight minutes to get to him. Both Amy's fight off a Handbot and then they reach the time portal but they can't get through to the gallery where the TARDIS is waiting. The older Amy realises that it has been locked externally and starts to override the circuits. As she does so a group of Handbots materialises. The older Amy fights them off and tells the young couple to go. The young Amy is anaesthetised by one of the robots and Rory has to carry he unconscious body into the TARDIS. The Doctor stands in the doorway as the older Amy runs towards him. He apologises and slams the door in her face.
The Doctor tells Rory that he lied: it would be too much from the TARDIS to contain both Amys in the same time stream. Rory objects and says that they can't leave one behind. The Doctor says that as soon as they leave the older Amy will cease to have existed but he says that Rory can choose which one stays behind. The older Amy and Rory say goodbye through the locked door. She tells him not to open the door or she will come in but she is giving the younger Amy her days with Rory as a gift. She steps away and asks the interface to show her a hologram of Earth. As she looks at her home and remembers how she fell in love with Rory she is anaesthetised buy Handbots.
In the TARDIS, Rory asks if the Doctor knew all along that he couldn't save both Amys. The Doctor says that he promised to save Amy and there she is, safe. Amy wakes and asks where her older self is. The two men look on in silence.