The first time Elizabeth Weir arrived in Atlantis, she lost her entire Expedition; the second time, she died to save them. This time, the Ancient scientist Janus has designed another failsafe to put right what went wrong. Sparky will endure. (Follows the first three seasons, and then diverges into a a sharp left.)
A little more happened during "The Long Goodbye" than John and Elizabeth want people to know. But you know Atlantis; no secrets there. Taking an alternate timeline after the episode, and all Sparky.