Headscratchers / Iron Helix

• The opening cutscene shows the Jeremiah Obrian was traveling with another Cerberus-class starship: the John Paul Jones. Why couldn't this ship be the one to stop the Obrian? It's obviously close enough, it was right next to the Obrian! It probably could've easily destroyed the Obrian long before it reached Calliope. And yeah, I know the answer is "because then there'd be no game", but still, it seems like such an obvious oversight in writing. Of course, I say "obvious", but it took me until writing this article to realize it myself, and I've been a fan of this game for 20+ years...
  • Given the circumstances of the extra special super secret mission that the Obrian was on, it's possible that the John Paul Jones was taken by surprise by the sudden change in course by the Obrian. Given how most militaries work, and the fact that the Obrian was almost certainly not responding to communication requests from the John Paul Jones, the likely next step from the John Paul Jones would be to contact military command to find out what's going on. That would take a while. By the time command realized that the Obrian just went rogue, and informed the John Paul Jones, the Obrian would have had a significant head start: presumably the John Paul Jones could catch up with the Obrian, but not until it was too late. The Indiana is implied to be able to catch the Obrian only because the Obrian would be passing by the Indiana on its way to Calliope.
  • Most likely scenario, given the ending and the ship's nasty cargo? It likely was no accident it went rogue, the JPJ was likely hung up in pursuit (or told not to pursue), and the ship headed towards the enemy world with their bioweapon. If the Indiana succeeded (the canonical ending), the lone crewperson could "disappear" easy enough with the ship's logs intact and all the data safe. If it hit Calliope? Well, they could write it off as a tragic "accident;" If the enemy bought the story, they would still be down a planet. If not? Well, they'd get the hot war they were after and a successful test of their bioweapon. No matter what went down, the people behind the bioweapon who want it used on the other guys won.