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In Atlantis' control room, the Daedalus' IFF was detected, indicating that the ship was in close proximity to the planet. However, the Daedalus was supposed to be on Earth at the time. Because of this, Lt. Colonel John Sheppard's team was sent up to the ship to, via Puddle Jumper, to investigate. Upon their arrival, they discovered the ship was actually from an alternate reality and used an Alternate reality drive to get to its current location. The ship had been continuously jumping between realities and then did so again shortly after their arrival. The second reality that the team jumped into was where this battle was taking place. (SGA: "The Daedalus Variations")
When they jumped to their second reality they saw an Unknown Alien ship firing down upon Atlantis. Lt. Colonel John Sheppard then ordered Dr. Rodney McKay to get the Asgard plasma beam weapons online so they could help the alternate Atlantis. Once McKay got the Asgard weaponry working, they fired upon the Unknown alien ship twice, knocking out its main weaponry. The ship, however, then sent out fighters towards the Daedalus. Sheppard quickly tries to give Ronon Dex a quick lesson in using the Railguns. While Ronon was attempting to shoot down the fighters, Sheppard attempted to pilot the Daedalus away. While Ronon fired against the incoming fighters, they continue to fire upon the Daedalus, easily penetrating its weakened shields, causing damage throughout the ship and inside the drive room where McKay cowered down to avoid the explosions. Ronon continued to shot down the fighters and finally hit one of their engines, causing the fighter to spiral out of control and crash into the Daedalus. The impact from the fighter combined with the shots from the other fighter knock out the Daedalus' sublight engines along with causing a hull breach.
In an attempt to flee the losing battle, McKay put into affect several protocols to increase the efficiency of the alternate reality drive. This caused them to jump to the next alternate reality much sooner. His plan succeeded and the Daedalus quickly jumped out of the battle. In the next reality, though, they discovered that the pilot of the fighter that had crashed into them had boarded the ship. After a quick skirmish with Sheppard and Ronon, they eventually killed it. With McKay's next plan to reverse the path they have traveled so far, the team learned that they will be plunged back into the reality with the Unknown Aliens. When they jumped back into the hostile reality, they found the alien ship right behind them. It quickly launched fighters towards them once they arrived. McKay got the sublight engines back online right before the fighters got in weapons range. They attempted to run from the alien ship, but they quickly gained on them. The fighters opened fire on the Daedalus and quickly knock out its sublight engines for good. Ronon attempted to return fire, but eventually lost his temper and began to bang on the console.
Suddenly, a new side appeared and began to fire upon the alien fighters. F-302 fighter-interceptors from the alternate Atlantis arrived and begin to pick off the unknown aliens. The alternate Lt. Colonel John Sheppard thanked them for taking out the flagship's main weapons, telling of how that saved them. As the unknown alien fighters were being destroyed, one of them began a collision course towards the Daedalus' bridge. Ronon attempted to fire at it, but could not hit it. Right before it would have hit the front window of the Daedalus, the alternate Sheppard took it out which caused some debris to hit the window, but it held.
After the alien fighters were defeated, Sheppard had a short conversation with his alternate self and they finally jumped away into the first alternate reality. They decided to make their way down to the hanger to get ready to leave the ship with the final jump. As McKay opened a door, they met with more unknown aliens. One of them fired and hit McKay in the shoulder. Sheppard and Ronon quickly moved in and took out the remaining aliens. As the last one fell, they heard a beeping noise coming from a thermal grenade that was dropped. They then quickly ran back out from where they came and dove out of the explosion. (SGA: "The Daedalus Variations")
The explosion from the alien's grenade caused a hull breach which prevented the team from reaching the Puddle Jumper in time. They attempted to think up a new plan and, once the Daedalus jumped back to their home reality, Atlantis sent a Jumper to them. Before the Jumper arrived, the ship jumped away and they discovered the team alive and floating around in Space suits. (SGA: "The Daedalus Variations")