Sheppard's team visits the planet Taranis at the invitation of two leading citizens, Dr. Norina Pero and Chancellor Lycus, who want McKay to repair a failing shield generator at an Ancient base they've discovered. Lycus also shows the team a massive Ancient warship, much like the Aurora, hidden in a vast warren of tunnels beneath the base. Although the warship is damaged and currently inoperable, Dr. Weir eagerly opens trade negotiations with Lycus as soon as she learns of its existence.
As mysterious earthquakes rattle everyone's nerves, McKay overcomes his attraction to Dr. Pero long enough to discover that her people have seriously overtaxed the shield's capabilities. Worse, the shield's energy source is the magma chamber of a supervolcano beneath the base - a volcano that has been destabilized by the excessive energy demands. A catastrophic eruption is now imminent: Half the continent is about to be ripped apart, rendering the entire planet uninhabitable. Everyone must evacuate.
As the earthquakes grow stronger, local villagers begin arriving at the base through the relative safety of the Ancient tunnels. Weir and Lycus lead some of them through the stargate to Atlantis, but seconds later, the ground around the 'gate erupts. The stargate sinks forever into a pool of molten rock.
From Atlantis, Weir immediately dispatches the Daedalus to Taranis, but it will require multiple trips to evacuate everyone. Sheppard and McKay, knowing that they don't have that much time, start repairing the Ancient warship while Teyla, Ronon, and Dr. Beckett hurry to a nearby settlement, to organize the first group of evacuees.
Soon after the Daedalus departs from Taranis, new vents erupt, ash starts falling, and the outside air turns toxic, forcing Beckett, Teyla and Ronon to send the remaining villagers through the tunnels to the warship. Then McKay discovers that a lava flow has sealed the main hangar doors shut. Now, even if he can repair the ship, they'll still have to find a way past this molten barrier.
Teyla and Ronon remain in the settlement until they've rounded up the very last of the villagers, only to be trapped when the tunnel that leads to the base collapses. As the duo fights to stay conscious in the deadly air, Sheppard notices that they're missing and descends into the maze of tunnels to find them. Soon he's cut off, too - and even if he somehow makes it back, there's still no guarantee that McKay can even get the warship off the ground.