Like Theodric said earlier in this thread:

As for the mysterious 'Shadowhunter'...could it be Gaius? I suspect it is, judging by his evasive tone and goals. That leaves the question as to how, exactly, he survived.


The more I think about it the more sense it makes, his skin did look pretty burnt (and Gaius kinda went up in flames back in the day), combine that with his hunting of Ascians (being, or at least feeling betrayed by them) and mentioning having dealt with the Scions before (us)