That's the only explanation. The first time he showed up and got "killed", it was so quick and pointless and stupid that you knew he'd be back in the end.
He didn't even die well. He just kind of shrugged and then deflated, like somebody let the air out of a life-sized balloon.
Pope was one of my chief complaints with the show. Largely because he kept doing the same story arc. He started as a jerk loner who hated everybody and worked against the team, and then learned to love, and then reset every off season back to jerk mode. I was actually pleasantly surprised when season 5 started and he wasn’t a jerk... then they killed his girlfriend in ep 3 and he goes SUPER jerk. Then we get that dumb plot line with him kidnapping the Mason kid, then he disappears and we run into him again and he’s turned into some half-assed Governor hosting gladiator contest. Then he gets half a building dumped on him. Some how survives that, crawls out without anybody in the 2nd Mass noticing, stumbles his way to the exact spot where Tom meets the Dornia, and dies. Every bad story telling habit they had went through Pope.
Then of course there’s the space marital aid the Dornia gave Tom to kill the queen (it even squirts virus out of one end, DUDE). That was hilarious. And he infects the queen and she blows up?! Yet still somehow infect all the other Espheni who also blow up?! Oh and it turns out the Espheni are getting revenge for their failed invasion 15 thousand years ago. So I guess we didn’t need the marital aid, Tom just needed to stab the queen with a pointy stick.
I could do hours on this show. It’s comedy gold.