Series 7, Episode 12: 'Nightmare in Silver'
"Doctor?" "Afraid not. I'm working the mouth now. Allons-y. Oh, you should see the state of these neurons. He's had some cowboys in here. Ten complete re-jigs." The Cybermen are back, and stronger than ever, attacking Webley's World of Wonder and converting the Doctor into their leader. Clara leads a punishment unit and the Doctor fights his new conversion in a chess match, as the pair battle to save Angie, Artie and the rest of the universe from a Cyber army.
Series 7, Episode 13: 'The Name of the Doctor'
"How are you even doing that? I'm not really here.""You are always here to me. And I always listen, and I can always see you.""Then why didn't you speak to me?""Because I thought it would hurt too much.""I believe I could have coped.""No, I thought it would hurt me. And I was right." The Great Intelligence kidnap Jenny, Strax and Vastra, taking them to Trenzalore. The Doctor travels to his own graveyard to save them, but the Great Intelligence jumps into his timeline, converting every one of his victories to defeats. Clara then saves the Doctor by following the Great Intelligence, and scattering herself across his life.