I don't remember a lot about this story, but without either of them having been pregnant (as far as I recall) an alien ritual ends up with them being presented with a baby, which the aliens refer to as a "gift". I believe the aliens expect them then to kill ("sacrifice") the baby to complete the ritual. Instead they take the baby back to Atlantis, to decide how to look after it(him?). Keller jumps in, and has it all planned out that she and Rodney will return to Earth to raise the baby. John protests, and it ends up that Keller is told to take a hike and he and Rodney make plans for how they will raise the child together on Atlantis.