First of all, stick a spy in there. Someone from the government trying to take down the resistance forces. I've only seen it in Tabletop games, like co-operative games with a defector, but that element makes it all much more interesting. Especially when you're trying to work out who the spy is.

Second of all ... (come on, think of something worthy of the A Team ... or Firefly ...) ... ok, one of your characters has been wrongly accused of murdering a government official, when the official has really faked their own death and undergone so much plastic surgery in order to infiltrate the organisation and bring it down, but this person was set up to cover everything up and you need to save them and, at the same time, find out who the spy is.