From the moment Jayce returns to the main Arcane universe, he knows what's going to happen. He and MageVik's chat must have been longer than that which we see on screen, something along the lines of, "It's all going to go to shit, but there is a chance you can stop it, and also get your Viktor back."
Jayce is not surprised to see puppet-Salo in the lower Hexgates room, nor that Salo is a puppet. "Have you given Hextech to the people yet?" he knows he's really conversing with Viktor. There's no reason for him to know this at this point, other than MageVik has told him everything.
All his actions from then on are to get to Viktor, by way of the Arcane Herald.
You can see when he takes up the kneeling position (a la the evolved Jayce in MageVik's universe) on top of the Hexgates, that he takes a deep breath, in a lets do this way.
"This is what you see?" Not, "what the hell happened?!"
Then, "we finish this together."
This is Jayce's rune, the last thing to disappear, the rest of Jayce having already been sucked into it. Not exploded or disintegrated, but slurped up by a small shard of glowing blue magic, which poetically, is back where the story started from.
All that's physically left is the corrupted hammer, but crucially, the Herald's body has gone as well, presumably sucked into the Arcane just as Jayce's was.
Until even the hammer's gone. Where Jayce and Viktor have ended up, however, is anyone's guess.
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