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Amnesiac Danny is wondering around the streets of Gotham and when Bruce comes across him, he thinks it's Jason; first as a hallucination and then after he manages to touch him, as some trick someone was trying to pull on him. Except… Danny even has the right clothes on! All muddy and dirty… Alas, when they check Jason's grave, there isn't anyone inside, leaving them with the wrong conclusion that Danny/Jason must have broken out of his grave.
DNA analysis is inconclusive. Every sample comes back as corrupted. Danny and Jason DO look the same and the similarities are convincingly enough to fool Alfred as well. Dick wasn't around too much, so at this point he also thinks Danny could be Jason.
Could, but the situation is… odd. Everyone is left standing wrong-footed. This Jason has no answers and all they have are a bunch of… hypothesis that they cannot test.
Even so, Bruce cannot help himself and tries to make Danny "remember". Eventually this leads to Danny thinking of himself as Jason, pointedly not thinking about how some things don't add up after he starts living in Wayne Manor.
And then enters Tim Drake, whose first act after being introduced is to say that Danny is a fake.