This is hard to talk about without spoilers, but I'll be vague enough to be useless without watching. Go watch it first, if you liked S1-2.
Every ep is resolving something from S1-2, there's almost no "new missions" as such. Everything has gone very wrong with the Faction taking over people, but that's more or less cleaned up, all the bystanders get mind-wiped and mostly don't recover their memories initially… But there's now Traveler conspiracy/support groups meeting. The boy from S1E3 returns, and I don't think a day of hanging out with a cop is gonna make a sociopath not 'path. Amanda Tapping as 001 returns, briefly, but then she's someone else again.
An AI that's been utterly useless so far gets upgraded, and the messengers aren't as safe as previously thought. Philip and the historians get a showcase episode, which mostly involves interrogating a dead man. The Trevor episode is somewhat annoying: If consciousness transfer works the way it has been described, the problem described can't happen, he'd be in a nice fresh brain every time.
In the only actual two-episode plot of the season, nuclear terrorism and data archives in the silliest possible storage medium, and a Wrath of Khan type ending for someone.
Protocol Omega somewhat contradicts previous explanations of how the Traveler program works, but some of the pieces from the season are assembled to get a hard reset.
I dunno if they're going to do a season 4. They sort of pushed parts together for it, and the last scene with Marcy & David suggests someone made changes already. But I could see them dropping it now and it's at some kind of a stopping point. I don't want another season like this, I want more of S1-S2 when it had plots.