In the distant past, the crew in charge of a fleet of ships celebrates their discovery of a habitable planet. In a cold hibernation chamber, Rem Saverem asks a young Vash where his brother Knives is. When Vash questions why everyone is in hibernation, Rem tells him of the Seeds Project. She explains that their ship is used to carry the seeds of humanity. Knives arrives, and they go to eat in the recreation room, which resembles an outdoor garden. They dream about making their new home into an Eden where crime and misery have no meaning. In the briefing room, we learn from Jo, the captain, that the crew’s old world had to be abandoned because it’s resources were exhausted. Later that night, Jo tells Rem he has no experience acting as a father and that she deserves the credit for the boy’s moral upbringing. The next morning, an engineer, Steve, complains about Rem’s time spent on recreation with the boys while he still has several days of work to do. When he discovers the kids finished his job while he slept, he angrily states that they are freaks for having grown this much in one year, and that they do not belong on the ship. Knives finds Vash crying because of the harsh comments from Steve. He flashes back to an event where Steve beat him for being in the cold room. This is followed by an even earlier flashback of the two boys as babies, with guns pointed around their incubation chambers and Rem blocking their line of fire. Rem decides to give Vash a new look when cutting his hair. When Knives’ turn comes, he decides to cut it himself, to separate himself from his brother.
The next morning, Steve drunkenly berates the rest of the crew for eating with the “freaks.” He beings groping at a female crew member, Mary. After being insulted by Knives, he stumbles out. As another engineer, Law, remarks to himself how much he hates Steve, Knives enters. We next see Knives separately enter Mary’s room. When Rem and the boys return to the recreation area, Vash spots a butterfly stuck in a spider web. Before Vash can free the butterfly, Knives squashes the spider, saying it was the easiest way to save the butterfly. When Rem and Vash explain to him that every life has value, Knives tells them that saving all the butterflies would starve the spider anyway. Vash tackles him and screams that he wanted to save both. Meanwhile, the rest of the crew has decided to place Steve back in cold stasis on the charge that he tried to force himself upon Mary in her room. Law later proposes marriage to Mary and jokes that he made a modification to Steve’s capsule, and he would not wake up again. He says that since he and Mary lied about the incident to get rid of Steve, they were now accomplices. Mary thinks he’s gone too far, and is killed after threatening to expose Law. Rem and the twins rush to the scene, and Law points the gun at Knives, saying that he is responsible for Mary’s death. Rem tries to calm him down, but Jo opens a hatch to eject Law into space after it looked like he was going to fire. Knives tells Jo that he made the correct decision, and then shoots him in the head. He then changes the fleet’s course to crash into the planet. Rem decides to stay behind at the last second, thinking that Jo is still alive, and sends the boys alone in an escape pod. From a window, Vash sees their ship explode upon hitting the atmosphere. Knives begins laughing and reveals his cleverly executed deception which led to the crew being killed. The rest of the ships switch into autopilot and engage proper landing procedure. In July City, 107 years later, Vash vows to take take care of Knives.
The whole mystery of the series was cracked open in this episode. It was full of clever metaphors used to illustrate how Vash and Knives viewed humanity in different ways. Knives views himself as superior and believed the human’s colonization mission was futile. He sought the quickest way to get rid of the problem, by killing them all. In contrast, Vash believes in preserving life at all costs. The technology scattered around the planet must logically be the remains of the fleet, which came down there over a hundred years ago. Vash and Knives are most likely the only ones remaining who remember the civilization’s true past. It can also be assumed that Legato is not the main villain if Knives is still around. Since Vash refuses to kill, the final confrontation between the brothers should be interesting.