They have been trying for a week to identify the right frequency and combination of radiation used to destroy them. Test number 375 works, and Julian Bashir and Miles O'Brien are ecstatic, and well as the other doctors involved in their destruction. Ambassador Sharat is pleased, and grateful for their work. But as he reminds them, that is only half the task. All data pertaining to them must also be destroyed, as well as the very large stockpile on each side.
Back at Deep Space 9, Commander Benjamin Sisko talks to the doctor, offering their congratulations. They are expected to be back the day after tomorrow, since there is a party on T'Lani Prime.
However, when they run the cycle on the final batch of cylinders, two Kellerun soldiers enter, and begin shooting. Bashir and O'Brien manage to disarm two of them, and get rid of all the soldiers, blowing out the genetic bath in the process. Unfortunately, all of the scientists were killed before they could react. When they cannot contact their runabout for a beam out, O'Brien transports them to the surface and sets the system to overload.
Meanwhile, Sharat and Ambassador E'Tyshra arrive at the station to give their condolences. They explain that everyone in that room, including many of their greatest scientists, were killed when Chief O'Brien accidentally set off a security device, and flooded the room with high-intensity radiation. Sisko doesn't believe it, but they show him the record of the internal security sensors, and ask him to extend their sincere sympathies.
Down on the planet, Bashir and O'Brien find a bunker, and hide there with their assault rifles, while Bashir opens a crate of medical supplies. O'Brien still can't figure out why the T'Lani would break their treaty. Either way, the way he sees it, they have to stay put; sensors will detect them if they make it a kilometer. They also find a very old com system, which O'Brien thinks he can get working – if Bashir will shut up and let him do his job.
Back on the station, the rest of the senior staff looks at the video. It shows things as they happened when the last cylinder was destroyed. But after that, O'Brien is baffled by a strange file which suddenly appears. He can't shut it down, when he tries cutting the power, a flash of radiation vaporizes them all. Odo wants to do his own investigation, Major Kira Nerys can't believe it, and Jadzia Dax tells Starfleet they need replacements for Chief Medical Officer and Chief of Operations. Sisko also has to go tell Keiko O'Brien what happened.
While O'Brien is fixing the transmitter, Bashir teases him about his being married with all the T'Lani women who would be running around. Bashir says marriage isn't fair to them with the lives in Starfleet they lead. The Chief, however, grabs a blanket, feeling quite cold. When Bashir scans him with the medical tricorder, he finds that his blood pressure is low, and he has a fever. He was near the genetic bath when it shattered, and he has been infected with the harvesters.
When Sisko tells Keiko, he doesn't have to say much. She can read it all in his face. He agrees to give her a copy of the recording, and there isn't much else he can do.
When the Chief's eyes get fuzzy, Bashir takes directions from him. His condition slowly worsens, almost falling asleep.
On the station, Kira and Dax talk about Bashir all night, and even Quark gives him a toast. The next day, Keiko comes up and asks to see Commander Sisko. She shows him, Kira, and Dax a part of the recording where O'Brien drinking coffee. According to the time index, it is late in the afternoon, and she says he never drinks coffee in the afternoon, because it keeps him up all night. She is convinced the footage has been altered. Sisko isn't sure, but he has Major Kira get the Ganges a day early, just to see what's going on.
Bashir finds the problem: the contacts on the sub-processor are corroded. He cleans them with a sterile pad. It is getting harder and harder for him to stay awake. He tells O'Brien about a ballet dancer he fell in love with, how they would finish each other's thoughts, and were crazy about each other. Her father even offered him a job as chief surgeon, but he didn't take it, because he couldn't have a Starfleet career. When he puts it back in the unit, they get power, but the transmitter still doesn't work. When O'Brien gets up to take a look at it, he falls right down again; he can't feel his legs.
As Sisko and Dax arrive to collect the runabout, Bashir gets the transmitter working, and sets it to a distress signal. O'Brien then gives Bashir his answer: marriage is the greatest adventure of them all. Sisko also examines the station where the accident occurred, and asks E'Tyshra about the accident, including if Sharat could have (hypothetically) modified the data clip. She doesn't see any reason why he would; the lasting piece is because both sides trust each other.
That's when Dax makes a discovery: an erased log in the Ganges computer reveals that a transport request was made 3 minutes after the fail-safe device supposedly went off, proving they were still alive at that time.
As O'Brien's condition continues to deteriorate, Bashir hears something outside. He grabs a rifle, and is surprised to find it is Ambassador E'Tyshra, together. When Bashir was about to explain that the T'Lani have broken the treaty, Sharat walks through the door, and they are both on the same side. After taking his weapon, they explain to Bashir that part of their destruction of information is killing the people who know it. Otherwise, they could be recreated by them, a risk they refuse to live with.
As they are about to fire, Chief O'Brien suddenly tells them to wait, and has Bashir help him up. As he is saying that it has been an honor serving with him, they are beamed away.
Bashir explains the situation as quickly as he can to Sisko. When he wants to send out a distress call, Dax says that there is a broad band inversion in place, wiping out communications and short-range sensors. Using this, Sisko plans a deception.
After refusing to release O'Brien and Bashir, Sisko puts the runabout on a collision course, forcing them to destroy it. When they are about to take the other runabout in tow, they find it is gone. All they can find is a federation warp signature. They conclude Sisko beamed aboard the runabout and piloted the first by remote.
Afterwards, Bashir and O'Brien are better friends, and Keiko is surprised to discover that O'Brien does in fact drink coffee in the afternoon. Meaning the discovery of the altered logs, and the entire rescue operation launched because of it, was by mistake.