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When all's said and done, with the Ancients and the Replicators both gone, Jack seeks out the son who saved his life.
He finds him in the Jumper bay, arguing with McKay.
“You flew it through a window,” McKay is saying, loudly and with passion, from the inside of a soggy, slightly damaged Jumper. “And then tried to drown us all.”
Sheppard, leaning against the wall where the door connected, smirked, “So it’s not working?”
“No it’s not working!” McKay says, letting out a noise that sounds slightly homicidal.
Sheppard doesn’t looked concerned, but must have spotted movement - or possibly heard or smelt him or something, it’s hard to tell while the other man’s senses remain a deliberate mystery to him - because he turns to face Jack.
“Sir,” Sheppard says, straightening a little.
“Colonel,” Jack replies and then glances over towards the direction of McKay’s voice. “How’s it coming?”
There’s an indistinguishable mumble from inside the Jumper - loud enough that Sheppard’s smirk says he heard him perfectly but not loud enough for Jack to make out actual words - that suggests McKay’s not impressed.
“It’ll be good as new soon enough,” Sheppard says with total confidence. “Any news from the SGC?”
“Weir will return as leader of the expedition,” Jack tells him. “And you as military commander.”
Sheppard looks surprised, “General Laundry threatened to court-martial me.”
“So did I, if you remember,” Jack says with humour.
Sheppard smirks, “Yeah. But I saved your life.”
McKay makes another annoyed noise, “Can you two go have this strange masculine bonding moment somewhere else?”
Sheppard’s smirk only widens but he gestures Jack away from the Jumper and the two of them stroll side by side out of the jumper bay.
“So I received an interesting call while you were away,” Sheppard says conversationally as they walk.
“Hmm?”
“Lieutenant Johnathan J. O’Neill Jr,” Sheppard says, making Jack stop walking. “He got injured in a training exercise a few weeks ago. Apparently I’m listed right beside you as his next of kin.”
“I didn’t realise he’d joined the Air Force,” Jack says.
Sheppard looks suddenly amused, “He didn’t. He’s a marine.”
Jack blinks at him in surprise, “Huh.”
“So a clone,” Sheppard says leadingly.
Jack sighs and continues walking, “How much did he tell you?”
“Something about an Asgard named Loki?”
“Yeah,” Jack says. “Junior was supposed to be an exact copy, but the Asgard did something to my DNA that made that impossible, so he came out like mini-me instead. Kind of made it hard for him to pass for me while Loki did all his experiments.”
Sheppard nods, “He said you two had some sort of deal?”
“No communication,” Jack admits. “Too weird, otherwise.”
“He has all your memories?”
“Up until the moment of cloning, yeah.”
“That must be weird.”
Jack shoots him a look, “Trust me - you don’t know the half of it."