Fics like Everything Ends: Once and for all

When a strikingly familiar universe vanishes while Jobu Tupaki is inside, the Doctor confronts her, believing her to be responsible. But soon they unveil a conspiracy led by the Disney Corporation and the SCP Foundation, working together to take over the entire omniverse for reasons unknown. On their travels, they meet some old and new faces, and Jobu has to learn how to care about people who are close to her, including her ex-girlfriend from the Alphaverse, a young trans boy who they rescue from SCP-4319, and Rose Noble, the Doctor's new protege who is far more important than she seems.

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