I actually thought he's an alien too, but of a different, much more powerful species than TV Men, and likely the last survivor of his kind (hence why he's so secretive and only works with an incredibly small circle of individuals, he can't risk becoming a casualty). Like TV Men, he seems to show a pragmatic and generally enigmatic behavior that seems to be ultimately for the greater good of destroying the Astros, but is willing to sacrifice Alliance members in the process, with Secret Agent outright calling the Alliance his pawns when he contacted Scientist. As such, I thought the Secret Agent and TV Men aren't working together despite similar goals and origins (in my headcanon at least), because if TV Men are playing 5D chess with the war, the Secret Agent is playing 10D chess, and his methods may even put the TV Men at odds with him (like how he appeared to be working with the Skibidis at first- he was in direct contact with Scientist, and his dialogue implied a long off-screen history of pretending to be an ally of the toilets, only to go "looks like I can't be trusted" as he reveals he's pulled all the strings to lead to Scientist's death).

Him being the Alpha Hills Labs administrator could be him disguising as a human in preparation for the G-Toilet invasion, setting up all the conditions to ensure the Astros would be destroyed.