The thing is, you can have one (or more) of the LIs be partially guilty without being the actual culprit, or in the way you expect. That's essentially the "Murder on the Orient Express" ending I alluded to.
For example, it's entirely possible that if a hacked Echo is the culprit, it could be Skylar and she was hacked in such a way that she doesn't remember committing any sabotaging acts. Or maybe Ishani did work for Synthstar and is partially responsible for some work that led up to the events, but she realized the full extend of what Synthstar planned and tried to defect and stop the actual culprit. So in a way, they both would be "guilty" but not like you might expect. In fact, Skylar being hacked and having her memory of it erased would mirror MC's amnesia and his own coming to terms with the bad things he did during it.
I do not think that the culprit is going to just be a classically "bad guy" to be found and punished or imprisoned. That's would be a resolution that feels far too telegraphed and out of character compared to every other major plot point so far, in my opinion. Think about the various character histories and arcs so far, including the MC. Almost all of them have degrees of moral grey and treat “villainy” as a symptom of control, trauma, or misunderstanding, not as inherent evil. The story consistently frames resolving conflict around empathy, autonomy, and understanding rather than good-versus-evil binaries. There almost certainly will be at least some unexpected factor or twist that mitigates moral culpability at least partially or else it would undercut that through-line that's developed the whole game.
What I expect will happen is that evidence will strongly suggest one of the LIs is generally a "bad guy" culprit (like with Ishani), but for some last-minute revelations to resolve it in such a way that it's clear they aren't a "villain", leaving Pandora without good motives to kill anyone. It's a classic pressure-valve and redirect approach to serialized storytelling. And based on what we know, I see a twist where either someone was hacked, blackmailed, or brainwashed into doing it, someone looks guilty but is secretly a double agent, or lots of people are guilty in small ways as the most likely way resolution that's been building. And possibly even an ending that includes elements of all of these.
