You can use them individually, or as a mob. A mob of four S.H.I.E.L.D. agents isn't a 4d mob, however; it's more like a 2d mob, a handful of minor characters. Because of this it may be easier to continue to treat them as individuals and just assign them one or two at a time. They can support the hero with dice just like any other character can. The hero can spend PP on them rather than have them use doom dice.
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Think I would use the SHIELD Strike Team from page BR32, just with different distinctions... or in non-combat situations or to keep it fast and easy maybe just as a d6 asset & and possible also as scene distinction. Guess depends on what the scene is all about and how the player would like to use them.
Disagreeing with this post just adds a die to the doom pool!
I let my players cash in the agents they bought in Breakout for free SHIELD resources. They stopped at the last SHIELD outpost before the Savage Land and used their agents' clearance to get some explosives, weapons, and communications equipment.