u/IkarugaDE

Regardless of the potential consequences for the story, I would like to propose the theory that Geno intentionally left Jones alive. I would go so far as to claim that he was already aware Jones would survive when he injured him and kicked him down the mountain:

• Geno could have killed Jones instantly; instead, he merely wounded him severely.
• He knows Jones's current location and that he survived, yet he takes no action against him.

While these points do not contain definitive proof on their own, a re-examination of the final seconds of the SHATTERED event reveals potential clues:

1. Geno only fired at Jones when the Dark Voyager flew in and entered the same room (after Jones had shot at the DV).
2. Jones stood with his back to Geno for several seconds - plenty of time to deliver a fatal shot. Instead, he only shot Jones in the right side of his back.
3. Only then did Geno reveal his identity, removing his helmet and show he is on the site of the Dark Voyager.
4. Geno kicked Jones down the mountain despite having already revealed his face; this was a moment when he could (or perhaps should) have eliminated him completely.

It is possible that Geno had no intention of injuring Jones or revealing his own identity until the Dark Voyager arrived. However, once Jones fired at the Dark Voyager, Geno was forced to act. Had he not fired, there was a high probability that the Dark Voyager would have killed Jones immediately. Furthermore, the Dark Voyager might have questioned Geno's motives when he spared Jones for "so long". The unmasking could have been an improvised act designed to demonstrate his ruthlessness to the Dark Voyager and to show that he was now definitively killing Jones - because he is now the only "enemy" who is aware of the Visitors true identity. Consequently, there was no reason for the Dark Voyager to further injure or kill Jones.

The fact that Jones is now regenerating in the pod - without the process being sabotaged or him being killed - could lend weight to this theory. In essence, Geno wouldn't even have to get his hands dirty: The Dark Voyager is incredibly powerful and evidently serves Geno with unwavering loyalty. Geno could simply send Dark Voyager to eliminate Jones, who would offer little resistance (from whom, anyway?).

We can only speculate about the precise motives behind this decision. If the theory holds true, it doesn't automatically mean that Geno is one of the good guys. He might intend to use Jones for future plans. Or, in a truly devious twist, he may have let him live because he loves the thrill because he doesn't know exactly when Jones will wake up and reveal everything.