Sheppard's team is trekking through the woods looking for an energy spike, when Rodney finds a door with an energy barrier. Sheppard tosses through a stone and it disappears. They poke a camera through on a stick to get a recording, while Teyla spots the words "Welcome to Ascension" nearby. They pull back the camera but there's nothing but rock corridors. Sheppard goes partway through and stops, but it starts to pull him through and the others are forced to let him go.
Sheppard is stuck in a dark corridor on the other side and can't make contact with the others. Rodney reviews the tape and realizes there is a time discrepancy – the camera shows two hours have passed even though it was only through the portal for a few seconds. Sheppard can't get back through, while McKay rigs up a test to determine the rate of time dilation – a branch thrust through for 20 seconds dies and rots entirely. McKay gets all the survival gear he can from the others and tosses it through, while Sheppard creates a fire, feels an earthquake, then finds the gear they tossed through.
McKay and Teyla then head back to the ship and rig more supplies as well as a camera for Sheppard to send a message. He then heads back to Atlantis to get more equipment and brief Weir and Beckett. Teyla comes back and tosses the gear through and sticks the camera in for three seconds. They pull it back but the tape shows that Sheppard is no longer there.
While McKay rushes to find a way to save Sheppard before he dies of old age, Sheppard has moved out into the local fields and encounters a man being chased by some kind of creature. The invisible creature hits him several times and claws his back open before going for the fleeing man. Sheppard recovers and leaps on it, driving it off and getting knocked out. Meanwhile Rodney and his team prepare to penetrate the time dilation that surrounds the valley to rescue Sheppard.
Sheppard meets with the villagers, who reveal there is no way to leave except to Ascend. The fleeing man, Avrid, reveals the portal was created so there was no indecision, and that they are there to meditate on their existence until they are ready to Ascend. Sheppard starts to bond with Avrid's sister, Teer. She warns the creature lurks nearby but won't enter the village, but later it appears on the borders and Sheppard prepares to confront it while the others take cover.
Teyla finds a sign on the tape indicating that Sheppard left. Sheppard is wounded after his second encounter with the creature, and a young girl, Hedda, heals his injuries. Sheppard is frustrated that the locals don't stand up to the creature. Months elapse and Sheppard finds some supplies back at the cave – Teer points out that Sheppard has friends in the village. She then notes she has precognitive visions and has seen he will lead them to Ascension.
McKay is confident he can shut down the time dilation field from the inside and he and the others go through. Sheppard attempts to point out that the natives are hiding rather then living, and that they will never Ascend like that. Then Teer announces that his friends have arrived…but the beast is attacking them. The team encounters the beast and even Ronon is helpless against it since it phases in and out of existence. Sheppard arrives to help them and the beast fades away. They brief Sheppard on the situation but then a giant version of the creature appears. Avrid and the others arrive to fight, and realize it is of their own creation. They band together and the creature fades away. Teer says the beast was the final obstacle they had to overcome, the manifestation of their own fears. She asks Sheppard to come with them but he refuses. As the others transform into glowing creatures, Teer says she will let them go through the portal but the sanctuary will remain for others who come – McKay reluctantly agrees and they head back.