Based on what the story has presented so far, we can make a few theories/assumptions...
-Dying in the real transports you to Eternum with your inventory intact. This is assuming it works in the same principle as being able to travel to Eternum without going through the standard login procedure. During the beginning of the Collector event we saw Orion didn't had clothes on, but he was able to fish some stuff out from his inventory to wear. Assuming this is the case then this supports the idea that Wyatt still has the gem that he had received prior to his death in the real, so unless the story points out later that he lost that upon his death and he did everything he could to get that stuff back then that's a reasonable assumption to make. Speaking of Wyatt...
-Wyatt/Thanatos could just simply track down the person with the gems in Eternum if he/she/they die in the real. Whether he's working with William (if Orion gets killed then this becomes a more likely scenario) or he's doing things solo (if this is the case then William might be waiting for Wyatt to collect the gems and eventually take him out to get the gems himself, which is easier said than done but at least it's technically easier to have just one target than several), there's no denying that the man has a way to track down the gems in the "game," so he could just simply track and hunt down Orion when he gets transported to Eternum.
BTW your preview pics show Astaroth - not Thanatos - talking to OIAL's MC in one of the bad ends. That said...
-Calypso is not a "weapon" that can be controlled. The story makes it clear that whatever we did back in Ogygia basically threw a wrench in that regard, given that Caly appears to be someone that is her own person (who may or may not have missing or fabricated memories...at least that's the vibe that Wyatt/Thanatos' words back in Ogygia and her "way too perfect" backstory of hers about Anima seem to imply) and is able to speak her own mind and act upon it. Still, it can't be denied that she has a sort of "bond" with Orion (Caly knows where Orion is in Eternum whenever he "logs in," and Orion is able to summon Caly (albeit he did so accidentally at one time, and I'm not sure if he'll remember doing so until a crucial moment in the story where he might need her)), which was likely established when Orion expressed intent to open the box and the box likely acknowledged since it was never shown that he touched it...
...well that, or the bond was already there and it'll be explained later on in the story why said bond existed long before Orion himself ever set foot on Ogygia.
Anyway, it's not made clear in this update's ending if William knows about that bond, or he's making the same assumption made by other players that she's some sort of weapon (but unlike said players he knows that Orion has her). We'll have to wait until later updates for clarification on that, I suppose.
