Sure enough, it's the T-1000, in the shape of Petty Officer Goodnow. "Who are you? What do you want?" asks Jesse. "Tell John Connor the answer is no," says the terminator, before reverting to liquid form and shooting up to the ceiling. Jesse hurries into the escape pod, and then we watch as the mini sub floats up from the Jimmy Carter which soon explodes. A ribbon of liquid metal shoots up through the water, over the escape sub.
In the present, Jesse strolls into her hotel room, carrying a plastic bag, and who should be waiting there but a grouchy John Connor, sitting in a chair, holding a gun. "If you pretend not to know me, I might shoot you in the head," he says, like nice welcome. He says they owe Riley the truth. "Don't you think?" he says, and stands up. "We owe the dead that much."
"You're John Connor," says Jesse, who then asks where the metal is. "If she were here, you'd be dead. You know that," John tells her. He calmly asks for her gun, since he knows she's not going to shoot him. She hands it over, and then John launches into a long, rambling soliloquy. I'm guessing a better reason for asking for her gun was so she wouldn't shoot herself rather than sit there and listen for five minutes as John gives her a little bit of the family history, and how future him sent people back to protect him. He used to wonder why he took the chance of sending a machine back (this would be Arnie in T2). "I don't wonder anymore," he says. "Human beings can't be replaced. They die and they never come back."
He says it wasn't Derek who told him, if that's what she's wondering. She's probably wondering, "How long do I have to stand here and listen to him prattle on?" He says Derek loves her. "You and me, we're the only things he has in this world," he says, adding sadly that Derek's like Riley in that way.
He says that she made mistakes, small things; a word or a phrase. "'Carrots and apples.' I'm guessing that's yours." He says when they were in Mexico, she heard his real name and ignored it. A man took his picture, and she destroyed it. "She put herself between me and a machine that was hunting me," he says. And he realized one day that she wasn't treating him like John Baum, but like John Connor.
Jesse finally breaks her silence to ask when that was. John's all, "I have to stare dramatically out the window before I can answer you." He shrugs and says he doesn't remember exactly, but it was a bad day. "Anyway, I started following her. The rest was easy. And hard." Jesse says Riley wanted to tell him. "I know. But she didn't."