The team travels to the home planet of the Durandanes, which the Ancients' database said were a wonderful people. However, once they get there they find a destroyed Wraith fleet in orbit about the planet and no life left on the planet from a 10,000 years old battle.
Upon investigation, they find the Ancients had set up a secret outpost there, and they were trying to build an experimental weapon using a power source that would make ZPMs look like alkaline batteries. The power source and weapon was a vastly larger version of the space-based weapon platform first seen in "The Defiant One".
As the team returns to Atlantis to tell their findings of the power source / weapon, Teyla prepares to travel to another planet, Balken, to negotiate for improved disease-resistant seed to help the Athosians' crops. Ronon asks to join Teyla, because he wants to escape the confines of Atlantis for a while.
During Teyla's negotiations Ronon threatens the person with whom she was negotiating. However, later on the planet, Ronon learns there is another survivor from his homeworld. This person tells Ronon that more than 300 people survived the attack on Ronon's homeworld. During this discussion, Ronon learns one of the survivors was a commander who was his mentor.
Back on the other planet, McKay winds up causing the death of a fellow scientist because he believed he could complete the job the Ancients started but failed to complete. Dr. Weir decides to terminate McKay's attempt to activate the power source and weapon, against the advise of Col. Caldwell.
McKay later pleads and convinces Sheppard to let him continue the work on the power / weapon. Then Sheppard and Col. Caldwell convince Dr. Weir to let McKay finish his work on the power / weapons system. However, after his own investigation, Dr. Zelenka vigorously fights against McKay's efforts to perform the second test, saying McKay is wrong.
While back on the trading planet, Ronon kills his mentor, after having Teyla to set up a meeting with him. Ronon tells Teyla that his mentor was a traitor who deserved to die. Teyla, upset over Ronon using her in his deception, tells him that she will never let him get away with that action again.
Back on Durandanes, McKay's second test of the weapon goes horribly wrong, and he can't shut it down. Sheppard is forced to evacuate the pair in their Puddle Jumper, avoiding the weapons fire they set off. They find Daedalus in orbit, and warn them about the impending destruction of the solar system, and both ships make it to safety before the solar system is destroyed.