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After his alleged suicide, Clay continued to exist as an AI recreation of his personality within the Animus. As such, he was able to manipulate much of the Animus' programming from within to aid another Animus subject, Desmond Miles.
He has all of the skills & physicality of Ezio & all of the intelligence & wisdom of Altair. He is also immortal in a sense that his consciousness is transferable from one body to machine & vice versa.