McKay and Zelenka are leading a crew of scientists through the formerly flooded areas of the city shutting down everything the Ancients activated while they were in control so that they can stop the power draining from the ZPM. They enter a small lab with an Ancient device. While trying to shut it down Rodney powers up the machine and is surrounded by a spiral of energy that appears to be DNA. He is checked out by Beckett and given a clean bill of health but Rodney is not convinced.
Later in the mess hall, Rodney overhears the team talking about him from the other side of the room. He discovers that his hearing has improved greatly and so he grabs his tablet, which has moved across the table into his hands, and walks over there and has a very minor rant. An announcement comes over the Atlantis PA system calling Sheppard and his team to the control room. There they receive a transmission from Major Lorne's team. They are under attack with enemy soldiers closing in fast. After they head out to start the rescue, Zelenka talks to Dr. Weir. He has discovered that the device is designed to manipulate human DNA.
Sheppard's team returns with Major Lorne and explain that Rodney thought wouldn't it be great if all their weapons jammed all at once and then it just happened. Dr. Weir does not believe him, and neither does anyone else, so to prove it, he uses his telekinesis to pick Beckett right up off the floor.
Rodney is in the infirmary hooked up to a vitals monitor, and a few other machines. Apparently there is a dramatic increase in synaptic interaction throughout all the sections of his brain, much higher than normal levels. Weir mentions an incident at the S.G.C where they found a highly evolved being in stasis, caused by altering of the DNA by a Goa'uld named Anubis, designed to artificially accelerate the human physiology to the point of Ascension.
Rodney stays a while in the infirmary, and then is let out with Ronon keeping him company. He discovers he can read people's minds, so he heads to Dr. Weir's office and asks permission to utilize the control chair of the city and reconfigure the power systems to increase the efficiency of the ZPM, as it will dramatically lower the city's power usage, and thus increase the ZPM's life. While he is fiddling with it, the lights in the lab where Zelenka is trying to fix the device go out. He heads to the control chair room to talk to Rodney, but Rodney is arrogant and keeps working. Zelenka heads back to the lab, very angry at Rodney. Weir is going over the research log that the Ancients left behind, in her office, when Sheppard walks in and asks how she's going with it, she says she's just getting to the "good bit" and Rodney may possibly Ascend. Sheppard leaves, but before he goes, Weir says that they need to talk to Rodney right away.
They walk into the control chair room and Rodney reads their minds. He realizes that if he does not Ascend near the peak of the evolution, he will die soon afterwards. He is faced with a choice: Ascend or die. At this point, a massive power surge starts going through the city and Zelenka is struck by a bolt of electricity and badly wounded. He is rushed to the infirmary and has a massive wound, in critical condition, with no pulse. Beckett prepares the paddles but Rodney tells him to move and Beckett protests that he is dying. He puts his hands above the wound and it begins to heal very quickly and is gone in a few seconds.
Rodney then goes on an inventing spree, inventing a new type of math, a way to increase the shield power on the Daedalus and designs a hyperdrive prototype for the Puddle Jumper. Weir tells Rodney that she thinks he is capable of Ascension and that he can retake human form if he chooses. He has the "Ascendameter" shipped from Earth to gauge his mental advancement. Weir has him take meditating lessons with Sheppard, because he lived with a group of people who were trying to Ascend for 6 months, to try and achieve the level of relaxation needed to Ascend.
After the first meditation session Rodney begins to believe that he is not going to Ascend so he starts working again. Weir tells him that he has to rid himself of guilt in order to fully concentrate on Ascending. He apologizes to Zelenka for being very mean to him during the past few years, and even calls him a "brilliant scientist." Zelenka is touched, and even a little confused as Rodney walks away. He also speaks with Teyla and helps her with the tea ceremony for the anniversary of her father's death. He comments that he knows you're not supposed to do it alone. Teyla appreciates this sudden and strange show of compassion and caring. He then finds Ronon and asks him about the scars on his back from the Wraith. He asks him if they are like a badge of honor or just a constant reminder of something he would rather forget. Ronon says he tries not to let the things he can't change bother him. Rodney hugs Ronon and squeezes him tightly for a few seconds, and then says he just healed them. He visits Weir in her office and finds she is still trying to figure a way to save him. He gives her a copy of a 500-page book he wrote for her about all the good things she's done.
Rodney gives meditation another try but it again does not go well. While talking to Sheppard he has a seizure and ends up back in the infirmary. Beckett tells him the advanced cerebral cortex is affecting the lower functions of the brain and his body is losing its natural ability to keep itself alive. Rodney and Sheppard have another go at the meditation, and Rodney slowly sinks to the required level of activity. He slowly goes to 1 Hz and suddenly his eyes open and he grabs Beckett violently. He lets him go and relaxes back into the bed with no pulse. Beckett says they need to bag him and get him on the ventilator. Weir protests, saying that he gave strict orders not to interfere. Beckett says Rodney just told him how to save him.
At the lab, they place Rodney in front of the controls. The machine is turned on, and Rodney is returned to normal. Apparently the device was designed to manipulate DNA, and it couldn't reverse the evolutionary process because everyone's DNA was different and it makes certain changes that cause the DNA to evolve in ways specific to the target's own unique physiology. Zelenka says that in order to manipulate the DNA to its previous state, the program required a precise reference point. Beckett says they keep blood samples from all the Atlantis team members for base-length comparisons. Rodney is back to normal, and is no longer "a dead man"; however he has regrettably lost all his newfound powers, including the ability to understand the theoretical work he did while he was "advanced." However, Rodney is recovered enough to give Weir a hard time about how she claimed to love him as he was dying.