Greg Rucka, the story writer behind Logan's Shadow, talked to IGN at Comic-Con about building Logan's Shadow's story. Interestingly, he was pitched to "salvage" the story and turn it into something far more substantial.
It didn't take long for Rucka to figure out that there was a lot of potential in the Syphon Filter franchise: it just needed to take advantage of the story elements introduced from the previous games. "Coming off of Dark Mirror and the stuff that had happened to the character there, I know of was stunned to be like 'Why aren't you using any of this stuff you set up?' I mean, he now has a kid! He knows that he's a dad! There's all this fabulous character stuff here. So, we discussed that and sort of tried to find a way to use the relationships that really have been building throughout this series and turn them into good story ... that's what we got here."
The story puts into serious question the loyalties of those around him. Although Rucka doesn't want to give anything away, it seems that he wants players to stay on the edge of their seats for yet another Syphon Filter beyond the next installment: "We got, I think, a good, good story for Gabe and I think at the end -- I don't want to give anything away -- it's got a nice ending. It's got the kind of ending that I think -- hopefully -- people will be like 'Where's the next one?'"