Few things fit the definition of "convoluted" more than a good spy yarn. You need to have a group that's in bed with another group which is seeking to steal something from a third group which is secretly run by a fourth group which is really just an offshoot of the first group to get the appropriate number of surprise twists into the story.
Sega clearly knows what they're doing with Alpha Protocol. The above video will introduce you to the assorted factions working with and against each other in the game. There's a bunch of them and, apparently, nobody actually gets along. Just the way I like it.