The OP is not bad, but the problem is Harry is an investigator (at heart) who couldn't be allowed to solve what he would investigate. The novel isn't from Thomas' perspective, or Ivy's or Lara's. Theoretically, all three might know about such a mission, but none of them could speak directly to the reading audience about what's going on and they could never tell Harry the truth either.
Those restrictions would make it very difficult for Jim; or any author really, to tell a satisfying story. There would have to be some kind of cover story to get Thomas off or put the blame on some bad guy who deserves to go down for some unrelated reason, while at the same time Jim would have to drop clues to us what was really going on. Of course, this would be confusing to more casual fans who haven't read the short stories or at least haven't read the specific short story that would give them the context they need to understand what was going on.
So points to g33k for coming up with a clever idea, but I just don't think it's a very workable one.