Dr. Rodney McKay gets "zapped" by a device, where his brain quickly evolves to that of the Ancients to achieve Ascension, and he gains super powers. However, he must learn to ascend, or he will die, but it isn't going to be easy.
In order to conserve power, Dr. Rodney McKay and a scientist crew (including Dr. Radek Zelenka and Dr. Rafaela Esposito) are heading through a recently flooded area of the city, shutting down systems recently activated by the Ancients during their short period of controlling the city.
In a lab, McKay powers up a machine and is suddenly surrounded and circled by a giant spiral of what appears to be DNA or some sort of energy (then subsequently gets hit by bolts of electricity from the machine) and stands there, surprised. Everything appears normal, except for the fact that McKay just survived a few lightning strikes with no damage to his body.
Later, McKay discovers that his hearing has improved greatly, and he overhears the team talking about him, 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 Lt. Colonel John Sheppard and his team to Stargate Operations. There they receive a transmission from Major Evan 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. Elizabeth Weir. He has discovered that the device is designed to manipulate human DNA (a DNA resequencer, presumably)
Sheppard's team returns with Lorne and according to McKay, the enemy attacking Lorne's team were defeated when McKay "thought 'wouldn't it be great if all their weapons jammed all at once?' and then it just happened". Weir, of course, does not believe him, and neither does anyone else, so to prove it, he uses his telekinesis to pick up Dr. Carson Beckett right off the floor. Everyone stares at McKay. Weir tells McKay to put him down, which he promptly does.
McKay is in the infirmary on a bed, 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 the brain, much higher than normal levels. Weir mentions an incident at Stargate Command "just over a year ago" where they found a highly evolved being in stasis, caused by altering of the DNA by a DNA resequencer by a Goa'uld named Anubis, designed to artificially accelerate the human physiology to the point of ascension.
McKay stays a while in the infirmary, and then is let out with Ronon Dex keeping him company. He discovers he can read people's minds, so he heads to 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 Zero Point Module, 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 DNA resequencer lab where Zelenka is trying to fix the device (it was damaged in the initial explosions/lightning when McKay had his DNA resequenced), go out. He heads to the control chair room to talk to McKay, but McKay is arrogant and keeps working. Zelenka heads back to the lab, very angry at McKay. 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 what she thinks might be the "good bit". Sheppard leaves, but before he goes, Weir suddenly reads something that worries her and says that they need to talk to McKay right away.
They walk into the control chair room and McKay reads their minds. He realizes what is happening: 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 – Zelenka is struck by a bolt of electricity and badly wounded. He is rushed to the infirmary and has a massive wound, in very unstable and critical condition, with no pulse. Beckett prepares the paddles. McKay tells Beckett to "MOVE!" and Beckett protests that "the man is dying!" and McKay says "I know, just give me a second". A look of concentration comes over McKay's face as he puts his hands above the wound. It begins to heal very quickly. In a few seconds the wound is gone. When the wound is healed, McKay is amazed that he could do it. In a panic, he runs out of the infirmary; probably scared of what other powers he has and to continue his scientific research into greater technologies.
McKay goes on an inventing spree, inventing a new type of math, a way to increase the shield power on the Daedalus, designing a hyperdrive prototype for the Puddle Jumper and figuring out why light behaves as particles and waves in quantum physics.
McKay goes through some emotional changes, realizing his fate is coming; he takes meditating lessons with Sheppard, who learned from the Ascension-seeking villagers he was trapped with the People of the Cloister, so that he will be ready when the time comes. 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 McKay walks away.
McKay also speaks with Teyla Emmagan and helps her with the "tea ceremony for the anniversary of her father's death." He comments that "I know 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, "When you think of your scars, are they like a badge of honor or just a constant reminder of something you'd rather forget?". Ronon responds "I try not to let the things I can't change bother me". McKay, somewhat amazed, answers that it's a healthy choice. Then suddenly hugs Ronon and squeezes him tightly for a few, for a surprised Ronon, too long seconds, then as he breaks away says "Hope you don't mind… I just healed them." He also typed out a book for Weir of all the "good things [she's] done". Elizabeth is utterly surprised that it's a massive 500 pages long, and wonders how he managed it with everything else he's been doing, but quietly touched that he did.
McKay and Sheppard try meditating, without much success as McKay just can't let himself go or keep quiet. Frustrated he gives up again, saying it's useless as he just doesn't know how not to be himself. Then asks Sheppard he'd like him to give his eulogy, something simple. He tells Sheppard he wants Beckett to do a full autopsy if any of the research will be helpful, and then to be cremated and have his ashes scattered in space. Then, he suddenly collapses, and Sheppard calls for a medical team.
Eventually McKay ends up back in the infirmary, as his body starts to die: the advanced cerebral cortex is affecting the lower functions of the brain and his body is losing its natural ability to keep itself alive. McKay and Sheppard have another go at the meditation, and McKay probably from the gravity of the situation finally slowly sinks to the required level of brain activity. They're all sadly standing around him and Weir tells him they all love him. He's surprised but accepting and looks pleased about it.
He slowly goes to 1Hz and suddenly his eyes open and he grabs Beckett violently staring intently into his eyes. He lets him go and collapses back onto the bed. No pulse. Beckett says they need to bag him and get him on the ventilator. Weir protests, saying "He gave us strict orders to... " and Beckett cuts in "No, you don't understand. He's just told me how to save him."
At the lab, Zelenka prepares the machine as they place an unconscious McKay on the floor in front of the controls, where he was resequenced before. The machine is turned on, there's another zap and McKay is returned to normal. Apparently (according to the now normal McKay) "The device was designed to manipulate one's DNA, and it couldn't reverse the evolutionary process because everyone's DNA is different, it makes certain changes that cause the DNA to evolve, in ways specific to one's own unique physiology." Zelenka cuts in: "In order to manipulate the DNA to its previous state, the program required a precise reference point." Beckett says "Fortunately we keep blood samples from all the Atlantis team members for base-length comparisons." They just had to input his original DNA as a comparison point. McKay 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", which frustrates no end. He and Weir discuss his recovery and note that it turns out he was very lucky - reading further into the logs Weir has found out that the machine's effects had been wildly unpredictable, and he could just as easily have been melted down into a pool of protoplasm. Weir has decided to forbid any future use of the device due to this instability, even though Sheppard keeps begging to be given a go, hoping for a bit of an 'upgrade'.
(Sheppard and Weir discussing the Ancient device activated by McKay)
Weir: John, I agree, this device may have great potential.
Sheppard: And with great potential comes great responsibility, I know.
Weir: Like a lot of other things we have found in this city, it is a very advanced piece of technology. For all we know, it could be very dangerous.
Sheppard: I am just saying...
Weir: Yes, you can be next.
Sheppard: Thank you.
(Weir sighs and turns back to working. Zelenka leans in.)
Zelenka: You know, if you're compiling a list, I'd...
Weir: Could we stay focused, please?
(Ronon and McKay are leaving the infirmary. On the way out, McKay uses his new telekinesis to snatch Beckett's doughnut)
McKay: You know, we could be a team. You could be my sidekick.
McKay: Yeah, it'd be, like, "Batman and Ronon." Has a nice ring to it.
Ronon: Yeah, you keep eating like that and it's going to be more like "Fatman."
(McKay has just discovered his newest power: the ability to read minds. He and Ronon go to Weir's office.)
McKay: Oh, I'm fine. No, yes, and it doesn't.
(Weir is in her office reading. Sheppard walks in.)
Sheppard: Well, how's it coming?
Weir: Actually, I think I'm just getting to the good bit.
Sheppard: Don't you hate it when people interrupt just when things are getting good?
McKay: Now, is Sheppard still bugging you to let him use the ascension device to turn himself into some kind of superhero?
Weir: Oh yes.
McKay: Despite the fact that the Ancient database states that its effects on people are wildly unpredictable and that I'm just lucky I wasn't instantly melted down into a pool of protoplasm
McKay: Huh. Well, maybe you should let him.
Weir: I think not.
McKay: If you're a highly evolved super-genius, put up your hand. (He looks around the Infirmary hopefully, then pretends to look surprised and raises his hand, smiling.) Oh!
McKay: Those scars on your back from your encounter with the Wraith, you know, with the tracking device? Are those, like, a badge of honor for you, or are they just a constant reminder of something you'd rather to forget? I mean, I know it's none of my business. I just...
Ronon: I try not to let things I can't change bother me.
McKay: That's very healthy. (Hugs Ronon, who awkwardly pats him on the back.) I hope you don't mind. I just healed them.
- Joe Flanigan as Lt. Colonel John Sheppard
- Torri Higginson as Dr. Elizabeth Weir
- Rachel Luttrell as Teyla Emmagan
- Jason Momoa as Ronon Dex
- Paul McGillion as Dr. Carson Beckett
- David Hewlett as Dr. Rodney McKay
- Kavan Smith as Major Evan Lorne
- David Nykl as Dr. Radek Zelenka
- Leela Savasta as Dr. Rafaela Esposito
- Donna Soares as Dr. Coleman
- Chuck Campbell as Chuck
- Colin Decker as Marine (Uncredited)
- Lalo Espejo as Scientist (Uncredited)
- Fraser Aitcheson as Marine (Uncredited)
- Hakan Coskuner as Medic (Uncredited)
- ? as Marine
- The episode is the second one in the series where the title references one of the main characters. It previously happened in "McKay and Mrs. Miller", making Dr. Rodney McKay the first character mentioned in an episode title more than once. His sister Jean Miller would become the second with "Miller's Crossing".
- The device shipped from Stargate Command was nicknamed the "Ascendometer" by Lt. Colonel Cameron Mitchell in the episode "Prototype", where it was used to analyze the evolution of a Goa'uld/Human hybrid, Khalek.
- The function of the device is similar to those used by Nirrti in "Metamorphosis" and Anubis in "Prototype", though both of those had a control panel separate from the genetic manipulation pedestal, suggesting that they were designed for genetic manipulation of other lifeforms. This device, however, would seem to suggest it was designed for experimentation on one's self. This may suggest that the Ancients in the Milky Way had willing test subjects, or the research was more accepted, while the Ancients in Atlantis were unable to find willing test subjects and forced to experiment on themselves.
- The plot of this episode parallels the story of Flowers For Algernon by Daniel Keyes. In Flowers for Algernon, Charly Gordon, a severely mentally challenged man, undergoes experimental surgery which gradually improves his mental capabilities to a genius level. Eventually however, the effects of the operation start reversing themselves, leaving Gordon unable to understand the studies and discoveries he made while enhanced (including the discovery of the existence and mechanism of his own procedure's flaw, which the procedure's original author failed to foresee). Similarly, McKay ends up unable to comprehend the bulk of the discoveries he made while evolving towards Ascension.
- Flowers For Algernon was published as a novella in 1959 and won a Hugo Award for best short fiction. Six years later, it was expanded into a novel and won the Nebula Award for best novel. The novel is considered a modern classic by many critics, and is fairly often discussed in high school-level literature classes. It was also adapted for the screen twice: for television in 1961 on the The United States Steel Hour starring Cliff Robertson as Charlie, and in 1968 as the movie Charly, again starring Robertson with Claire Bloom, earning Robertson the Academy Award for Best Actor.
- Also, Flowers for Algernon is told solely through a series of the protagonist's diary entries which first depict his evolution into a genius, and then his deterioration; this is paralleled by the use of video logs in another Atlantis episode featuring an alteration of McKay's mental status, "The Shrine", where McKay's ability to think progressively worsens to the point of dementia (due, in this case, to parasitic infestation).
- Unlike McKay in that episode, in Flowers for Algernon the protagonist eventually dies as a result of the procedure's failure. This is in fact the title reference: Algernon was the name of the lab mouse on which the procedure was first tested. The mouse dies before the protagonist; it is implied he knows from then on he will ultimately share the mouse's fate. In the last line of the last diary entry, being the last line of the story, the protagonist asks his nurse to put some flowers by the place the mouse was buried in the institute's yard.
- When McKay reads his last EEG reading at the end, he states he had reached .03 hertz. The readout shows he'd reached 1 hz before suddenly grabbing Beckett and telling Beckett how to save him. The EEG monitor does not show any decimal places.
- Dr. Carson Beckett's donut is from Tim Hortons, a Canadian coffee shop chain, originally founded by NHL player Tim Horton, before his death in a car crash.
- Even though it aired before, this episode was actually filmed after the episode "Sunday", making this Paul McGillion's next to last episode to film for this season. The last episode he filmed was "The Ark".
- Dr.Radek Zelenka refers to the events of "The Return, Part 1" and "The Return, Part 2", Lt. Colonel John Sheppard refers to those of "Conversion" and "Epiphany" and Dr. Elizabeth Weir refers to those of the Stargate SG-1 episode "Prototype".
- This is the first episode of the series in which Anubis is mentioned.
- The equations on McKay's whiteboard after he becomes super-intelligent are almost verbatim copies from the textbook String Theory, Vol. 1 by Joseph Polchinski.
- The "unused brain capacity" myth (common in fiction and first seen in Stargate in "The Fifth Race", also see the page for that episode) returns in this episode and is heavily utilized throughout. It is, in fact, not true that humans (or any other known organism) would have large portions of the brain that are left unused. The myth is instead probably due to a misinterpretation of an early 20th century psychologist's assertion that many people never take the time (or never get the opportunity) to develop (as in, through normal methods like learning, self-improvement, etc.) a good portion of the mental potential they are born with.
- The sound effect used for the energy pulse from the Ancient device is remarkably similar, if not identical, to the sound effect used for the energy weapon on Ori warships.
- McKay jokes with Ronon Dex that he could be McKay's sidekick saying they would be like "Batman and Ronon". Jason Momoa co-starred in the film Justice League fighting alongside Batman as Aquaman King of Atlantis.
- This is the first appearance of Major Evan Lorne (Kavan Smith) since he commanded the Orion in the premier episode of Season 3 "No Man's Land". Kavan had been unavailable due to shooting The 4400 where he played Agent Jed Garrity.
- Once again one of German Atlantis crew member can be seen sporting his German flag patch upside down. It is evident approximately at (0:30) on the uniform of one of the scientists, while the researchers are moving along the previously flooded parts of Atlantis.
- At the beginning of the episode (1:53), just before Dr. Rodney McKay turns the device on for the first time, the ancient display is not flat, but made of canvas.
- Around the 2 minute mark, when McKay is fiddling with the controls, we can see the controls under his right index finger shift and pull out as he removes his finger.
- Near the end of the episode, with McKay near death, Lt. Colonel John Sheppard is standing with Dr. Elizabeth Weir on the right side of the bed. From a different camera angle he is shown on McKay's left, then again on his right.
- In this episode Weir and Sheppard both comment on how he helped Ancients ascend in the episode "Epiphany". The people he helped were Human (although from an unspecified advanced society in Pegasus), not Ancients. The People of the Cloister Ascension retreat from that episode clearly referred to the Ancients as a people distinct from and predating themselves.
- When McKay is leaving Dr. Carson Beckett's lab and snatches the Doughnut from across the room watch closely as the camera shifts to him as he walks toward the camera, for a moment you can see that he already has the doughnut in his left hand and when the camera pans away from his right hand to the doughnut on the table you can see him move just slightly as he shifts the doughnut to his right hand so it looks like he brought it across the room.
- When Weir is talking to McKay about helping him ascend, the "electronics" in the background is labelled "SGA/BLU02" or "Blinking Light Unit 02".
- Hungarian: Rodney, a szuperhős (Rodney the Superhero)
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