After discovering Janus' secret lab in Atlantis, Dr. Rodney McKay and Dr. Daniel Jackson unknowingly activated a signal alerting the Vanir to their location. After a successful surgical strike on Atlantis, the Vanir captured McKay and Daniel, as well as took a key component of the Attero device. After they were forced to activate the device, its purpose became apparent as two Wraith cruisers in Todd's alliance were destroyed upon entering hyperspace. An unforeseen side effect of the device was the destruction of all active Stargates with the force of 12 Naquadah enhanced Nuclear warheads, which was shown when Atlantis' Stargate exploded.
Believing that he had been betrayed, Todd hijacked the Daedalus and, after making a quick stop at Atlantis, set a course for M6H-987, the planet where the Attero device was located with the purpose of destroying it. Meanwhile, Lt. Colonel John Sheppard and Dr. Radek Zelenka hooked up with a Traveler generational ship, captained by Katana Labrea, with the intention of arriving at M6H-987 before Todd and the captured Daedalus. (SGA: "First Contact", "The Lost Tribe")
Ronon Dex and Dr. Jennifer Keller managed to avoid capture and set out to disable the Daedalus. The two made it to engineering and Ronon disabled the hyperdrive, weapons and shields by shooting the control crystals for them. Todd's crew managed to repair shields and hyperdrive, but couldn't get weapons back up, so Todd had the ship programed to search for the facility where the Attero device was and to crash into it once the ship dropped out of hyperspace. They then held up in their Wraith scout ship and waited for the ship to drop out of hyperspace at which time, they would depart the ship.
Meanwhile, Katana Labrea's ship successfully engaged and destroyed one Vanir spaceship, another one fleeing into hyperspace before its shields could fall. Ronon then rescued Keller and the rest of the Daedalus' crew and regained control over the ship's systems as it descended though M6H-987's atmosphere. Lt. Colonel John Sheppard flew the Traveler ship in front of the Daedalus and opened a hyperspace window big enough for the two ships, jumping them safely to the other side of the planet where the remaining Vanir spaceship was destroyed by the Traveler ship. Major Kevin Marks then finally managed to regain control over the ship's systems. The Daedalus subsequently beamed up Dr. Daniel Jackson and Dr. Rodney McKay from the facility, and the Attero device was destroyed by the Traveler vessel. (SGA: "The Lost Tribe")
After the battle, both Katana Labrea's ship and the Daedalus returned to Atlantis where whatever damage they sustained was repaired. As Atlantis' Stargate was destroyed, the Daedalus retrieved one from the currently inactive McKay/Carter Intergalactic Gate Bridge. After being hit by a bolt of electricity from the Attero device, Dr. Daniel Jackson was sent back to Earth where he would make a full recovery. (SGA: "The Lost Tribe")
Following the destruction of the Attero device, the Vanir began attempting to save their species by forcing an Ascended Asgard named Ran to descend, hoping that she would be able to provide them with the genetic material they need to repair their race. This brings the Tau'ri back into conflict with the Vanir, but a peaceful resolution to the conflict between the Tau'ri and the Vanir is achieved when the Tau'ri aid the Vanir in contacting Ran directly from a shrine on Earth and she agrees to descend and aid the Vanir in saving their race. Afterwards, the Vanir promise to cause the Tau'ri no more trouble. (SGA: "The Third Path")