Ep 6. The Shrine

John Sheppard, Ronon Dex, Rodney McKay, and Jennifer Keller land on the planet MX7-245 in search of a ZPM (Zero Point Module), the most powerful power source in the universe, needed to power the city of Atlantis. The planet's inhabitants are not welcoming, but the team discovers a lab where a project was conducted to create nanites that would help humans achieve their full potential by accessing parts of their brain that are not normally accessible. The team investigates further and learns that a scientist named Malcolm Tunney was working on the project and his partner, Andrew, was injured, leaving him with memory problems. The team finally finds Malcolm's diary and believes that they may be able to use the nanites to help Carson Beckett, who has contracted the Hoffan drug virus, which is causing his body to gradually shut down.

The team returns to Atlantis with the nanites and a plan to use them to help Carson. Rodney and Jennifer use a modified version of the device to inject the nanites into Carson's brain, but instead of waking up from his coma, Carson has a severe mental breakdown and becomes convinced that everyone hates him. Carson eventually disappears, and the team believes that he may have returned to the planet where they found the nanites. The team deploys a search party, but Rodney is struggling to handle the situation after seeing Carson's mental state severely deteriorate. Rodney becomes even more upset when he discovers that the malevolent aliens from the planet are actually nanites themselves, and they have taken Carson as their queen. Rodney feels responsible for what has happened to Carson and becomes obsessed with finding a way to save him.

Rodney eventually realizes that the key to saving Carson is to connect with him on a personal level, and he uses a device to transport himself into Carson's mind. Once inside Carson's mind, Rodney discovers that Carson is living out his greatest fear of being forgotten and alone. Rodney works to show Carson that he is still loved and important to the team, and he eventually convinces Carson to return to Atlantis with him. Upon waking up back on Atlantis, Carson has no memory of his experience with the nanites but appears to be recovering from the virus.

The episode ends with Rodney reflecting on his experience and acknowledging that he was not prepared for the emotional toll that Carson's illness had on him. He decides to take a break from his work to recharge and spend some time with Jennifer. John and Ronon are happy to have their friend back and praise Rodney for his bravery and determination.