Clay isn't entirely deleted during Revelations, and the team manage to reassemble his data while in the Grand Temple. He's given his own computer system/network to dwell inside to avoid another deletion incident with the Animus.

So, Clay ends up being a helpful part of the modern team, being present in every way but physically, whether he communicates through speakers or on-screen text. Catching up with William and Rebecca? Passive aggressive conversations with Juno?

In the end though, he manages to tamper with the Grand Temple in the same manner that Juno used the computers to send e-mails, and manages to conjure up a hologram body too.