Progeny

"Progeny" is the fifth episode in the third season of Stargate: Atlantis.

Synopsis
The Atlantis expedition makes first contact with the Asurans, who claim that they are the last of the Ancients. However, after holding the team prisoner, they learn that they are not people, but machines; Replicators, and they plan to destroy Atlantis.

Plot
After discovering an Ancient outpost, Dr. Elizabeth Weir joins Lt. Colonel John Sheppard's team on a mission to Asuras, a world inhabited by a society of millions. They are an advanced people, and it doesn't take the team long to conclude that they are (unascended) Ancients. Their leader is Oberoth, a powerful, arrogant man.

The team also meets a more quiet, sensitive Asuran leader named Niam, who brings the team before the Asuran Council. There Oberoth explains that they are an off-shoot from the Ancients who long ago inhabited Atlantis. Though their race was once united, the Asurans left when the Lanteans did not heed their counsel during the war with the Wraith.

Weir and Sheppard challenge Oberoth about the persistent threat of the Wraith, and are amazed to hear that the Asurans have a plan to completely eradicate them, but he will not share the details with them. Oberoth is curious, however, when he learns that Weir's team has set up a base of operations in the Pegasus Galaxy, though she is careful not to reveal that it is Atlantis. She hopes the Asurans might spare some Zero Point Modules in trade, since they are able to make them and have an abundance of them.

The negotiation doesn’t go well, since Oberoth believes that the Atlantis team has nothing worth trading for. But he is surprised to find out that Weir requires a ZPM, and suspects the city is of Lantean design. Unable to get a ZPM, Weir and her team plans to leave the Asuran city.

But when the team is ready to depart through the gate, Oberoth shows his true colors. The team is restrained and put in a holding cell, however, they are able to easily escape. Stealing a Puddle Jumper, the team dials Atlantis, arrive safe and sound. Soon, though, Atlantis comes under bombardment from 7 Wraith Hive Ships, and 15 more are on the way. Weir orders them to dial Earth and set the self-destruct. However, automated systems were damaged in the initial strike. Unable to give themselves enough time, Sheppard stays behind to activate the auto-destruct.

But just as the auto-destruct is about to go off, Sheppard wakes up: his mind has been probed by Asurans, who now know the gate addresses of both Atlantis and Earth. Sheppard, surrounded by his unconscious companions, and still in the cell, is surprised that they are still on Asuras, but a horrified Dr. Rodney McKay reveals that they never left. What's more, the Asurans are not humans: they're similar to Human-form Replicators. When the rest of the team awakens, Niam reveals that they are in space. The Asuran city is an Ancient city ship, and they will finish what they started, destroying the original home of their creators.

The Asurans, as Niam reveals to Weir, are not biologically Lantean. They are artificial lifeforms that evolved from an experiment to create nanites to attack the Wraith on a cellular level ("Hot Zone"). But the microscopic creatures came together to form increasingly larger and more complex organisms, eventually imitating their creators to become human in appearance. The Asurans begged the Lanteans to remove the aggression program, but they refused, having put safe guards up, and desperate for a weapon. When the Lanteans realized their experiment had gotten out of hand, they attacked this new race with their fleet of warships and nearly wiped them out.

McKay suspects that the Ancient experiment may have been the genesis of the Replicators that SG-1 and the Asgard battled in our own galaxy. But Niam is not like Oberoth. He is one of a few among them who still wishes to imitate his creators, to reach ascension, but killing the inhabitants of Atlantis surely cannot help them reach enlightenment. Niam believes that the only way it is possible, is for McKay to rewrite their Base code. In return, he will stop Oberoth from attacking Atlantis and help in Earth's fight with the Wraith. McKay manages to successfully reprogram Niam, but the team cannot trust Oberoth to call off the attack. Because of this, the team decides to destroy the city before it can reach Atlantis. McKay succeeds in reprogramming Niam by overwriting his aggressive nature. Then he stumbles on a major discovery.

McKay sees that the Asurans are connected through a subspace network and inserts a glitch that will paralyze all of the Asurans. The team takes advantage of this by programming the ship's ZPMs to overload. Unfortunately, the Asurans begin to override the glitch and try to stop the team. They manage to escape on a Puddle Jumper with Niam, and destroy the Asurans before it attacks their city, but the Asurans remotely reset Niam in retaliation. The reset Niam reverts to his aggressive nature and attacks Weir, forcing Sheppard to launch him out into space. On Atlantis later, they discover that the Ancients either deleted all records of the Asurans or hid them very well. Despite the victory, they know the Asurans are likely rebuilding and will come again.

Goofs

 * When Lt. Colonel John Sheppard is having his mind probed, he gets in the Puddle Jumper without his vest, but in the next shot he has his vest on.
 * Possible plot hole goof: The Replicators expressed that although violence was in their programming that they could not harm The Ancients, their creators. The Ancient Gene exists in most of the Atlantis Team whether inherited or implanted. It should have been impossible for the Replicators to harm them, or the many Ancient Gene carriers on Atlantis itself. Although, this programming may have only extended to physical harm rather than mental harm, or even only those specific Ancients who had created them.