I still don't know where Jordan was, but in the end he was there shaking his head about how Clarke and company blew up a society that was happy in their delusion. Like father, like son.
Diyoza's daughter comes out of the anomaly and stabs Octavia, who then disappears.
I didn't actually know this was the season finale, but the events pointed that way. I guess they did "better" in the sense that they didn't kill everyone in Sanctum and they are technically free of their false gods. Crazy Russell is the only prime left, I guess. The Dark Commander is in the Eligius computer, I assume. Finally, people give a crap if Octavia dies. Abby is also all the way gone, which was inevitable.
I have to wonder if they go to any (or all) of the other planets next season, especially since it's the last.