On Earth, a woman contemplates her daughter playing with a train set. The woman starts scribbling on her daughter Madison's art pads and working out elaborate mathematical formula as her husband arrives home. The woman, Jeannie, discusses it later with her husband Kaleb and he suggests she send it in to her superiors. Jeannie continues to work until Samantha Carter arrives to ask her about it. On Atlantis, Sheppard tells McKay that Carter needs help with Rodney's sister… Jeannie.
Rodney arrives back through the Stargate to wonder what trouble his sister has gotten into. Sam shows her the proofs and he reveals she dropped out of the fast track and became a mother. Rodney would rather implement the proof with Sam and leave Jeannie out of it, because Jeannie is giving them trouble. Sam insists Jeannie help and Rodney relents and brings her flowers, but Jeannie doesn't believe he's sincere. Jeannie refuses to sign over her rights to the military until Rodney tells her what's going on. Rodney meets Kaleb and Madison and is invited to dinner.
Afterward, Rodney tries to convince Jeannie to go with him without much luck, and finally has Sam beam them both up to the Daedalus. She's clearly impressed and later Kaleb advises her to go… and she agrees.
The Daedalus leaves orbit although Sam has to stay behind to deal with other business. She explains about his Project Arcturus and his attempt to draw zero-point energy from parallel universes and create unlimited energy. They hope to use Jeannie's proof to create a bridge to another universe. Jeannie worries they may endanger the people in the parallel universe but Sam reassures her that the odds are infinitesimal that the universe they select at random is inhabited. En route they work out the calculations and send the plans on to Dr. Zelenka to set up.
The Daedalus arrives just as Zelenka has the mechanism set up. Everyone is eager to see Rodney's sister and they proceed with the experiment as the sibling rivalry between the two continues. They take a break but that night a foreign object materializes in the chamber. It's… Rodney and he wants to speak to the person in charge.
The "real" Rodney arrives to find Jeannie talking with Sheppard and his team and sharing memories about Rodney's childhood. They're summoned to the isolation room where the new Rodney (henceforth "Rod") is being kept. Rodney and Jeannie talk to Rod, who tells them that his universe is endangered. They came up with a plan to beam someone, Rod, into the anomaly in their universe using an alien force field for protection. Unfortunately there's no return for him as the matter bridge is one-way.
Rod and Sheppard bond over a game of golf where Rod reveals Sheppard is an immodest genius. Later Rod bonds with the rest of the team but they get an emergency report that Zelenka had to turn on the matter bridge to prevent a catastrophic overload. They determine entropy could wipe out Rod's universe and work to stop the process. As they work, Rodney doesn't want Jeannie to hang around Rod and they have another round of brother-sister squabbling. Jeannie is unhappy with how Rodney doesn't respect her.
Rodney wonders if Rod is lying to them but Sheppard figures that he's jealous and Jeannie likes Rod more. Rodney is called to the containment chamber where Zelenka and the others pick up a transmission from the other universe--they have a solution to the buildup by flooding the exotic particles through the tear but it will destroy Atlantis and rip a hole in their galaxy, swallowing it up.
They have six hours before the "other" Stargate go ahead with their plan but Jeannie comes up with a plan to send a burst of energy with the ZPM to destroy the bridge, but it will reduce the amount of energy they have to travel back to Earth. They have no choice--Weir agrees.
As they work out their plan, Rod suggests that he uses his force field to try a dangerous transport back to his universe. He's loved by (almost) everyone in Atlantis, but he'd rather head back to his team no matter the risk. The bridge starts to collapse but they can't cut the power without endangering Rod. Rodney times it as close as possible but the ZPM module is still depleted.
Later Jeannie watches a tape of Rodney leaving a message for her from a few years back, where he apologizes for not being there for her. Rodney comes in as Jeannie prepares to leave. Rodney can't quite get an apology out but he at least manages a hug and asks if she's happy, and they make plans for Christmas. Later Rodney arrives in the cafeteria to find the team talking about Rod and admit they find him a little creepy. Rodney's more then glad to hear and sits down to gossip with the team.