A sudden thought...

That WF agent in the mission in the ammo development facility we raided had a false ID chip.

Since when did the Fed have false ID chips?

Presumably he got himself inducted as a Rank 1 agent with the Ai-Jinn and got it then.

Though that raises further questions of why they didn't notice his original chip...

Someone was probably bribed not to notice. Maybe at some point over the next few weeks, I'll take a look over precisely who was hiring him - see if I can uncover anything further.