Superheroes seem to form their own communities, their own strata in society. Given that some of these people have the power of a nuclear bomb, it's understandable that certain espionage, police, and security agencies would want a mole in the superhero community.
The easiest types of supers for a non-super agent type to simulate are martial artist-gadgeteers and armoured-suit guys. (Actually, the agency may not have the budget for a *really good* armoured suit; I ran it with a martial-artist gadgeteer as the mole.) And having a secret ID is a good excuse for wandering off at odd times (and making reports to superiors).
The problem begins when the mole goes native. He forgets about making reports, he forgets about his loyalties, he's just caught up in the entire experience of being one of the Good Guys and thumping the Mauve Marauder. He ignores a recall order, so the Agency sends people in to collect him.
The PC's can be the agents sent to collect the mole, or they can be other supers, who are helping to defend the mole without knowing quite what's going on.
If you need to make things more confusing, there's the fact that he's been recalled because his ID has become known to other Agencies, and they want to capture him (in the guise of a supervillain, perhaps) and wring his brains about that little escapade in Bangkok four years ago, or the defection of Gyorgi Dimitrov, or whatever suits your political inclinations.