Teyla is discussing her feelings for someone with her friend Dr. Hewston and leaves her to go get her sparring rods. An explosion rings out behind her, killing Hewston and leaving shrapnel in Teyla's side.
Three Hours Earlier
Mike Branton approaches Weir and after some work persuades her to join him for a lunch get-together… which isn't a date. She goes to Teyla to apologize for breaking their lunch date and Teyla understands. Beckett notices her after she changes into civilian clothing and notes he and Rodney are going fishing on the mainland. Beckett figures she has a hot date but quickly figures out it's none of her business.
Weir and Branton have lunch then go out to watch the ocean and he asks to meet with her again. They end up kissing but Weir quickly stops, claiming any kind of serious relationship would split her focus. She gets a summons to the control room where she hears about the explosion that injured Teyla.
Five Hours Earlier
Sheppard approaches Teyla to remind her she and Ronon were going to learn golf from him. Teyla quickly bows out claiming she has mission reports to file, but that excuse doesn't work for Ronon when he tries to get out. Sheppard ends up trying to explain the sport to Ronon, who is bored with the concept but has no trouble hitting drives. Beckett arrives to announce he's going fishing with Rodney. Ronon then invites Sheppard to a stick-sparring match combined with capture the flag. Sheppard doesn't do very well, so they end up relaxing by drinking beer and listening to music. Ronon admits he isn't dating anyone and hedges about who he left behind. Talk turns to Sheppard's marriage and whether he might get together with Teyla, but they're interrupted by an explosion. Sheppard and Ronon go to investigate and find Beckett tending to the wounded, including a badly injured Teyla. Dr. Zelenka reveals that according to witnesses Hewston just blew up from within.
Fourteen Hours Earlier
McKay is berating Hewston and another scientist, Watson, about activating an alien device and finally relents, and Beckett reminds them about the mandatory rest day. The next day he goes to visit Dr. Brown in the greenhouse and tries to find a way to get out of fishing with Beckett by asking her on a date. She's tied up with her work so he heads up to the mess hall and runs into Beckett. He (badly) tries to get out of the fishing expedition and Beckett finally relents. He gets together with Dr. Brown for lunch and discuss their awkward relationship after Rodney's possession. Rodney admits his exposure to his sister and family made him think of getting married, but not to Brown. Awkwardness ensues and Rodney wonders why she's attracted to him. They're interrupted by the explosion and Rodney calls Sheppard and the others to reveal that the device Hewston activated is an Ancient weapon prototype that creates explosive tumors in human beings. They figure they need to find Watson, unaware that Beckett has him in sickbay after the explosion.
Two Hours Earlier
Beckett leaves Rodney and tries to get Zelenka to join him. He's in a chess match and asks for a rain check. Beckett then tries to get Major Lorne to join him but he's busy painting. Finally he heads back to sickbay and talks to his assistant Dr. Cole, and gives her the day off because he has a headache. He's tending to a patient when the explosion goes off, and quickly mobilizes emergency teams. He takes Teyla into surgery and stabilizes to her, then starts working on Watson. McKay gets hold of Beckett and sends an ordnance disposal team, but Beckett refuses to leave his patient. He orders everyone else out although one nurse insists on staying to help Beckett remove the tumor.
Beckett seals the sickbay and begins the operation, refusing to listen to Sheppard and the others' attempts to get him to leave. Beckett finally gets the tumor out and puts it in a carry case, then unlocks the sickbay. The ordnance man moves in with a bomb containment unit but Beckett takes it and goes to meet the team. He gives it to the ordinance man… just as it explodes, killing them both.
Later McKay is packing up Beckett's quarters when Ronon arrives to offer help. McKay will be going back to Earth to tell Beckett's family, and feels guilty over how he let Hewston and Watson check the machine. Sheppard visits Teyla in sickbay and helps her walk to the memorial despite her injuries. Weir presides at the memorial and gives a stirring eulogy, then bagpipes are played as the Stargate is activated and Sheppard, Ronon, McKay, and the others take Beckett's body is sent back to Earth.
Later back on Atlantis, McKay watches the ocean and communes with Beckett's spirit. McKay admits Beckett was the closest thing to a best friend he ever had and Beckett tells McKay not to blame himself. Beckett disappears as McKay says goodbye one last time.