"Weather" follows the activities of an Ultra, Inigo, whose ship Petronel is attacked by pirates. The ship is almost wiped out, but a piece of debris destroys the pirate ship. Inigo discovers a Conjoiner girl hiding on the ship. Van Ness, the Petronel's captain, allows Inigo to go and find her. She initially refuses to come with them, but Inigo knocks her out with a tranquilliser dart. Inigo's captain insists that she be kept restrained in a radio-shielded cell, as he is convinced that she can control the ship. Inigo talks to the girl who tells him that she cannot tell him her name – as a basic human, he would not be able to process it. She describes it as like the atmosphere of a gas giant, so he gives her the name of Weather.
Inigo continues to speak to Weather as often as he can, but his captain refuses to let her out of her cell. He tells Inigo that he hates Conjoiners (whom he refers to as "Spiders") because in the war against them, they took his wife and turned her into a Conjoiner without her consent. When the two met later on, she no longer seemed to hold any interest in him. Weather tells Inigo that the Conjoiners considered the act a kindness, but failed to realise the effect it would have on loved ones of the people they transformed. Meanwhile, the ship detects an incoming stealth vessel. Inigo, being the shipmaster, is in charge of the engines, but finds that he cannot make them accelerate without danger of nova (this happens if the engines are pushed too hard, if non-Conjoiners attempt to open a Conjoiner Drive to reverse-engineer it, or if the two engines on a ship are allowed to get more than 1 mile away from each other). He gets permission to let Weather look at the engine, but she insists she cannot do anything to help.
Weather speaks to Inigo's captain and repeats a message his wife left for him in the Conjoiner group memory. He lets her further inspect the engines. She opens one up and takes Inigio inside. They discover a brain that the Conjoiners inserted into the engine: it has to calculate the engine's workings to control the energy the drive produces, but has taken damage and cannot process enough information. Weather merges with him, making Inigo promise to bring other Conjoiners to help when they reach their destination. Inigo admits his love for Weather and leaves the engine.