The Return, Part 1

The Return, Part 1 is the tenth episode of the third season, as well as the 50th episode of Stargate Atlantis.

Plot
With Atlantis' Zero Point Module depleted, Rodney McKay and Samantha Carter devise an ingenious solution to solve the problem of transportation between the Pegasus and Milky Way galaxies. Using 34 Stargates from both galaxies, Stargate Command has constructed a massive chain of Stargates between the galaxies that would reduce the time to travel between Atlantis and Earth from three weeks to thirty minutes. The test is successful, but after John Sheppard returns from the test, McKay detects strange readings on the Daedalus's sensors.

Upon closer examination, McKay finds out that the anomalous contact is actually an Aurora class warship moving close to the speed of light. McKay hypothesizes that the ship is a damaged Ancient battleship making its way from Atlantis to Earth, but because its hyperdrive is damaged, it is forced to move at near lightspeed. Though the trip would take millions of years, relativity from moving close to the speed of light would mean that only a few years would pass from the crew's perspective. The implications of this would mean that there could be living, breathing Lanteans on board.

The Daedalus manages to make contact with the ship, the Tria, and transport the Lantean crew, numbering roughly a hundred survivors, back to Atlantis. The Lanteans are overjoyed to see that their city is still intact, but reveal shocking news. They intend to reclaim the city and ask the Tau'ri to leave. Gen. Jack O'Neill and Richard Woolsey arrive in Atlantis to try to negotiate, offering manpower, resources and infrastructure to help the Lanteans make Atlantis great again, but the Lanteans' position is steadfast. They acknowledge everything the Tau'ri have done and the debt they owe them, but say they need time alone after ten thousand years and that at some point in the future, they will be welcomed back.

With no support from the Lanteans, and with an Ori invasion of the Milky Way galaxy to deal with, the Atlantis expedition is disbanded and returned to Earth. Teyla Emmagan, Ronon Dex, and the Athosians are relocated to another planet. Everybody attempts to deal with their sudden separation from Atlantis in their own way. Sheppard is assigned to lead one of the SG teams, McKay is reassigned to Area 51 and Carson Beckett is given a surgery post at the SGC. Elizabeth Weir essentially drops out of the radar and becomes a virtual hermit until Beckett coaxes her out to have dinner with the others.

Meanwhile, back in Atlantis, O'Neill and Woolsey (who the Lanteans welcomed to stay as ambassadors) report that an Asuran ship was detected, but the Lanteans are confident that they won't be harmed, since the Asurans' base programming prevents them from doing so. Unfortunately, the Lanteans are taken completely by surprise when the Asurans suddenly attack and invade Atlantis.

Sheppard, McKay and Weir are summoned to the SGC. After hearing O'Neill's final transmission, Gen. Hank Landry decides to send the Daedalus to Atlantis and destroy the city with a nuclear warhead. With the gate bridge in place, the Asurans could use it to gate to any planet in the Milky Way, which the SGC cannot allow. The four Atlantis expedition members told of this are horrified at the news, and hatch a daring plan to try to save O'Neill, Woolsey, and Atlantis. Before anybody at the SGC realizes it, the four steal a cache of upgraded Replicator disruptors (calling them "Anti-Replicator Guns" or ARGs), hijack a Puddle Jumper, and use the gate bridge to travel to the Pegasus galaxy.

On the new Athosian homeworld, Teyla and Ronon are approached by Ladon Radim, asking them to consider working for the Genii. After Radim leaves, the two discuss this: Ronon has no desire to join the Genii, but Teyla comments that he may not be happy as a farmer.

At that moment, Sheppard, McKay, Weir, and Beckett arrive, and recruit Ronon and Teyla to help retake the city. With the team assembled, McKay uses a special backdoor program embedded into the Stargate's programming to open a wormhole to Atlantis and disable its Stargate's shield. Sheppard then flies the Jumper straight through the gate, uncertain of what is waiting for them on the other side.

Notable Quotes
General Landry: Colonel Sheppard, I'm going to assume you're still at the Midway Station waiting for Dr. McKay to rewrite his macro. I understand what you're doing, Colonel - Hell, I'll even call it brave, but if you don't turn that ship around immediately and come back to the SGC, I'll see to it personally that your career in the military is- (Sheppard slaps a button, disconnecting the communication) Sheppard: That way I won't know what he was gonna say.

McKay: They emit a directional energy beam that disrupts the connection between nanites. Ronon: Not what I asked. McKay: Yes...they work good. Ronon: Good.