When we last caught up with him, the Doctor had embarked on a quest to find Clara Oswald. The Bells of Saint John mysteriously opens with a man claiming that human souls are being uploaded to the internet through a special Wi-Fi network.
Meanwhile, the Doctor has gone to a monastery in Cumbria in the year 1207 to try and work out what exactly is going on with Clara. He's interrupted by "the bells of Saint John," which causes the Doctor to take a horse down to a cave where he has hidden the TARDIS. Things get even stranger when the TARDIS's exterior phone begins to ring; and guess who's on the other line? None other than Clara, asking for help.
The Doctor arrives just in time to stop Clara from being uploaded by a robot disguised as a girl. A Miss Kizlet, apparently the one behind the uploadings, is informed that the Doctor has intervened as they feared he might. Kizlet sends another robot after the duo, before causing a plane to come hurtling down towards them. The Doctor and Clara manage to board the plane using the TARDIS, revive the crew, and keep it from crashing.
The Doctor and Clara attempt to work out what's really going on, with Clara using her computer expertise to track the uploaders back to their base. Unfortunately, it turns out a bunch of the people in the cafe were actually under the control of Miss Kizlet, and a distraction from a robot disguised as the Doctor allows Clara to be uploaded.
The Doctor isn't taking any of that however, and rushes to the uploader base on The Shard, demanding that Miss Kizlet release everyone she has trapped. Of course, she refuses, until the Doctor reveals that he is actually still back in the cafe, and that he had sent a mobile robot server in his place. The server uploads Miss Kizlet, trapping her in her own network, and forcing her to allow everyone free to escape herself.
Unfortunately, it turns out that Kizlet had been working for the Great Intelligence this whole time, and they are not happy. They wipe the memories of all the uploaders, including Kizlet, just as UNIT arrives to arrest everyone.
Meanwhile, the Doctor asks Clara to travel with him full-time, which she initially refuses, before telling him to come back the next morning, as she may have changed her mind by then.
The story picks back up in "The Rings of Akhaten," with the Doctor investigating Clara's past. After discovering her mother died when she was young, the Doctor returns to her as promised, and asks where she wants to go. Clara decides she wants to be shown "something awesome."
The Doctor decides to take her to see the titular Rings of Akhaten. There they explore an alien marketplace that uses items of sentimental value as currency. After accidentally getting separated from the Doctor, Clara meets a young girl, Merry, who says she is hiding because she is nervous about having to sing at an upcoming ceremony. After some reassurance, Merry and Clara head to the ceremony.
Merry was right to be afraid though. The song she was singing is meant to keep an evil god her people call the Grandfather asleep. It is thought that if the song is interrupted, the Grandfather will awaken and devour the universe.
As you might expect, things don't go smoothly when a mummy awakens and kidnaps Merry. The Doctor and Clara rush to the rescue where they find the Mummy trying to consume Merry's soul. The trio manage to escape, and it's revealed that the Grandfather is actually the entire planet itself. The Doctor realizes that the Grandfather feeds off of memorizes and feelings, and attempts to overfeed it by giving it his Time Lord memories. This isn't enough though, and it's only when Clara gives up the leaf that caused her parents to meet that the monster is defeated.
At the end of the episode, the Doctor returns Clara home, and the two seem to part ways, at least for now. The story will pick up in "Cold War" next, with the Doctor clashing with one of his oldest foes.