Shadowhunter is Gaius beyond any reasonable doubt.
- He has Gaius' mask
- He uses Gaius' moves Quickstep and Terminus Est from the Praetorium (though these have been used by others also)
- He wears his long gunblade across his back (which is less common)
- He recognises Alphinaud and says he has “history” with the Scions
- He is a racial Garlean who looks to be in his fifties (like Gaius)
- He has reason to have a vendetta against Ascians
- He has his arm bandaged as though burned
- And even his colour scheme is reminiscent of Gaius.
Natsuko Ishikawa, a main scenario writer, when asked about the possibility of Gaius’s survival prior to patch 4.3, said that they would “depict a resolution” to this unanswered question in the near future. (
Source)
In a Dengeki E3 interview, Naoki Yoshida responded to a question regarding Shadowhunter’s identity by saying that they intentionally made the hints clear, and that they don’t intend to betray our expectations. He said that he also explicitly asked for the final zoom in on the mask to be made really obvious. (
Source)
Aaaand then Michael-Christopher Koji Fox, when being asked about how they write big lore revelations, had this to say:
I did not retcon. I did naaaht. Oh hai, Gaius.
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Source)