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Remember, Joker is loose after TDKR since Bane opened Arkham and Blackgate and all those (actually did he open Arkham?). Anyway Blake is the new Batman.
So the Joker went back in time to steal John's report card because that will lead to a chain of events that will lead to him not losing his dad. Remember, he tells Bruce that his dad died when he was 9. He's 9 in the comic.
Now remember, his dad was shot when he was 9. That's because they went out to celebrate all his As and the shooter was there. Without the report card, they won't go out to celebrate and his dad will live, leading to him never going to that orphanage and never seeing Bruce Wayne, and never figuring out his identity, and never inheriting the mantle of the Batman, etc.