While investigating, undercover, the nature of an addictive corn-like crop grown on P6G-452, found by accident by SG-3, SG-1 got into a firefight with members of the Lucian Alliance. After SG-1 retreated to the Stargate, Dr. Daniel Jackson attempted, in vain, to dial out only to have the gate beamed mysteriously away before he could finish. Having nowhere to retreat to, SG-1 was captured and Worrel, leader of the local Lucian Alliance faction, suspected them of the theft with Worrel even going so far as to torture them in the hope of getting SG-1 to admit their guilt despite the team insisting time and time again that they were not guilty.
Meanwhile on Earth, Major General Henry Landry learned from the Tok'ra that someone had been stealing Stargates all over the galaxy. He suspected Ba'al but needed proof. Therefore, he turned to the imprisoned former follower of Ba'al, Nerus who was being held in Area 51. At the same time, after several failed attempts to establish a lock with the planet SG-1 was sent to, the newly-commissioned USS Odyssey led by Colonel Paul Emerson was dispatched to rescue SG-1.
At Area 51, Nerus confirmed Landry's suspicions and told him that Ba'al was likely trying to establish a new empire with the gates. Following a sizable feast provided by Landry, Nerus admitted to have developed a way to disable a Stargate's correlative update system, effectively rendering one undetectable to the network. Ba'al's plan was to set up his own network of Stargates on his own planets, then use the Dakara superweapon to wipe out the rest of the galaxy using the original Stargate network.
Meanwhile on P6G-452, Worrel was about to execute SG-1 when they are beamed aboard the Odyssey and filled in with the latest information on Ba'al's scheme. Nerus requested his freedom in exchange for the coordinates to Ba'al's location, but Major General Henry Landry was reluctant to accede. As he knew better than to trust a Goa'uld, Landry secretly fed a subspace locator beacon to Nerus and then agreed to release him.
When Nerus finally returned to Ba'al's Ha'tak, the beacon transmitted his position to the Odyssey. When trying to use his technology with Ba'al's ship, a computer virus created by Dr. Bill Lee executed, disabling the ship's defenses and rendering it blind to the arriving Odyssey. SG-1 then beamed aboard the ship, made their way to where the stolen Gates are stored and began planting locator beacons on them so they could be detected and beamed aboard by the Odyssey.
Not everything went smoothly, however, as the Lucian Alliance detected Ba'al as well, and three Ha'taks began firing on Ba'al's defenseless vessel. Ba'al quickly managed to restore his shields, preventing Odyssey from beaming out SG-1 and the Stargates. With Jaffa closing in, SG-1 used one of the Gates to return to Earth, apparently disabling its locator beacon to do so. Soon after, Ba'al's shields failed, allowing the Odyssey to beam aboard all but the Stargate SG-1 used. Moments later, the ship was destroyed and the Odyssey, not battle-ready, escaped into warp when the Lucian Alliance vessels targeted them.
The Odyssey returned to Earth where it later became battle ready, and SG-1 returned to Earth through the Stargate where they were later debriefed. Presumably the Odyssey returned all of the Stargates to the planets they belonged at.