They never discover why Earth stops responding, why the Gate persistently fails to connect, why the Daedalus never comes back.
The ZPM's depleted but it lasts just long enough to let them panic, then mourn, then finally make plans. John's missions become searches for refuge, echoing that first chaotic day before the failsafe activated and Atlantis rose. Their last act before leaving through the Gate is to submerge her again: Rodney sets the timer.
The remaining Athosians come with them, too few to survive alone, their skills sorely needed now.
The planet's uninhabited, temperate, thickly forested from Ancient terraforming, with fertile soil in the valleys. They chose it for that, and the deep limestone caverns for storage and shelter.
Rodney complains the caves make his bones ache so John shares his bedroll. One change, lost in many - rules that once governed them now meaningless.
Tents are pitched and cabins raised, the botanists supervising land clearance. John leads trade missions, hunts, and plows, while Rodney builds. An aqueduct from the river, a water mill, pumps.
Twenty people die the first winter: illness, injuries. They learn to kill lion-bears and wolf-lizards.
Nightly, John's hands mourn Rodney's belly. They're all weathered, whipcord thin.
Spring, and John's plowing.
He looks down.