With The City of Atlantis having left it's old homeworld, damaged by the Asurans Gate Weapon, Weir struggles between life and death having been grazed by the beam. In the meantime McKay must try to find out why the city dropped out of hyperspace before reaching the new homeworld.

As things start to look severe for Weir, McKay realises that they only have a day at most before the shields fall, and things become even harder as the City realising what is going to happen, starts turning off the Gravity and collapsing the shields to a more shorter area in order to maintain it for longer.

With the City nearing power levels lower than that necessary to jump into hyperspace, McKay and Zalenka rush to try and fix the hyperdrive engines. However trouble is never far away, as they soon discover that their course will take them through an Astroid belt, and with Shields not protecting most of the city, it would mean the city being destroyed.

Taking a huge risk, Sheppard takes all those with the Ancient Genes into the Puddle-jumpers in an attempt to clear a path through the Asteroids.