The way Tom ended up on minecraftia is actually kinda goofy?? I like to think that the galaxy is huge and that it should be extremely rare for 3 different lumians to have somehow ended up on the same little planet by mere happen-chance, so I don’t think Tom randomly crashed here. Xeph disappeared from home planet several years ago, but I like to imagine instead that Tom was dispatched with a small team, acting as their commander (hence the yellow uniform) as they set out to find their missing militarymun. He was their captain, yea, but kind of a garbage one!! very on brand— he sent every member from their ship off in a pod so they could split up and search faster(assuming they have some sort of tech to locate other members of their species), and then realized a week later that he didn’t actually send them off with any means of communicating back to the main ship? So it was just him, and it’s a bloody miracle that his tech happened to locate lumian life on this planet called minecraftia, except he’s not great at flying the ship either so he ended up half-crashed.
Which is not a big deal! Because Xeph was a prodigy, he was stupid smart and one of their best guys, he’ll know how to fix the ship and get us back home, right! Xeph: haha jokes on you I actually don’t have any memories from before from my crash sorry m8
So Tom’s located xeph, mission accomplished, but he’s basically stranded on this planet now. And he doesn’t know anything about minecraftia, definitely doesn’t really want to be here, but Xeph more or less shows him the ropes, adopts him into the leading yoglabs workforce, and they become pretty good friends! Amicable at worse. Tom actually builds a good portion of yoglabs and is really well acquainted with both Xeph and Honeydew at the start!
It’s only as time goes on and xeph becomes more wrapped up in Yoglabs power that Tom gets more and more brushed to the side— Xeph had opped him, trusting that, as Tom doesn’t know anything about this planet and has plenty to do working for Yoglabs, he should have no reason to leave or discover how much power xeph actually gave him.
As far as Honeydew goes, he and Tom were actually really close! It’s weird, bc Tom ended up closer to Dew, especially the more that Xeph got wrapped up in yoglabs secrets and experimentation. The only real turning point here is after the clone incident, Honeydew was never... quite the same? They grew apart after that point, so Tom was kind of slowly alienated from them.
Ben, on the other hand, wasn’t really allowed to see or visit anyone other than the scientists leading his project? Honeydew certainly wasn’t typically allowed back into the chambers where they kept test subjects. The only reason Tom knew of him was due to routine check-ins.
In the end, after all’s been said and done and Tom and Ben have escaped, dew’s more happy than he is sad to lose a friend. He doesn’t entirely understand what it was all about, but they seem happier, sooo so be it! Hopefully that answers all of ur questions! :) y’all are welcome to send in more (pls send in more) if you’re curious!