The actress told The TV Addict that Amy Pond's "undying faith" in the Time Lord could be challenged.
"Many things are happening to this girl that could really damage her," said Gillan. "She kind of really idolised The Doctor in the last series and many things have happened that could damage that."
She hinted that the 11th episode of the current series, Toby Whithouse's 'The God Complex', will explore the relationship between the pair.
"It's really, really exquisite and it's really explored in episode 11," she said. "It is something they explore with [the episode's monster] the Minotaur and it's really, really interesting. And something happens that changes that completely."
Gillan also claimed that she is not concerned about being typecast by her Doctor Who role.
"I really hope to do a variety of things after Doctor Who," she admitted. "Actually, I think there's a lot of variety in the show, so you get to show a lot of different aspects."
Doctor Who returns to BBC One this Saturday at 7.10pm and airs the same day at 9/8c on BBC America.
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Watch Digital Spy's interview with Karen Gillan below: