The parallel of Arlo saying, "It’s all up to them (John, Sera, and the trio) now," in the s2p2 recap and John saying, "He's (Arlo's) always been one of us," in 366 is just... so striking.
John sees all six as an "us" and thinks of Arlo as a necessary member. (I don’t ship Jarlo, but that line really makes me see the appeal). Right before our eyes, John went from "us" (him and potentially Sera) vs "them" (the hierarchy, represented by Arlo) to "us" (the main six, including Arlo) vs "them" (the authorities and the injustice in the world).
Arlo sees the other five as a group, one that can go on without him because, well, he was never all that close with them anyway. He didn't really have any friends throughout s2, what with Rei dead, Remi mad at him for being in the authorities, Blyke and Isen siding with Remi, John being John, and Sera wrapped up in Spectre stuff. He doesn't realize that to the rest of the main cast, he's part of the group. I think, when they come for him and he gets his memory back (in whichever order that happens) he's going to be very surprised that they even bothered.