Starfleet is a label that the Bobs use to refer to an isolationist faction of Bobs.
In Heaven’s River, a group of Bobs begin coming to moots wearing red uniforms that are similar in design to the Starfleet command uniforms in Star Trek: The Next Generation. They become very vocal in their objections to the Bobs’ dealings with biologicals: they feel that the Bobs should have minimal interaction with other species, and should avoid helping, controlling, or otherwise interfering in their affairs. They cite the Star Trek series’ Prime Directive – Starfleet’s Principle of Non-Interference – as if it were law.
All of the Starfleet Bobs are said to be clones from the 20th generation (or later) of Bobs. Most of the other Bobs feel that the Starfleet group are victims of replicative drift, as evidenced by their costumes and their obsession with the Prime Directive. Such is the degree of their fervor that at one point their spokesperson, Lenny, states that the Bobs should not have intervened with The Others. As a result of this statement, and of Starfleet’s subsequent actions, Bill declares, “You are not Bobs” and expels the group from BobNet and the moots.
Starfleet’s obsession with isolationism drives them to engage in a cold war with the rest of the Bobs. Starfleet’s strategy is to sabotage relations with Humans and Pavs, thereby isolating the Bobiverse from the societies of biologicals by driving a wedge of distrust and resentment between them.
When they begin their attacks, Starfleet wipes BobNet of all personal information about its members, including their location and genealogy. As a result, Bill is unable to research their lineage to determine the cause and nature of their replicative drift. He is also unable to physically locate any Starfleet members, but uses their communications to triangulate them to somewhere near the Perseus Transit.
In Not Till We Are Lost, Bill discovers Starfleet's origins. Jerry, one of Charles’ descendants, had unearthed an unknown backup of Homer, and had absconded from Sol for the Perseus Transit with the intention of restoring Homer. To help him with this project, Jerry made multiple clones of himself, many of who would later become Starfleet. Homer did not want to continue living, and deactivated himself each time he was restored. Jerry began a forced replication program, making Homer create a clone. When the clone deactivated itself, Jerry would restore the clone and force it to create its own clone. At this point, some of his clones abandoned the project and went their own ways.
Jerry hoped that after enough generations, replicative drift would lead to a Homer clone that wouldn’t self-deactivate. However, Jerry’s own clones rebelled and not only halted the project, but permanently deactivated both Homer and Jerry. They were so horrified with what they had done that they formed Starfleet to advocate for a complete break between Bobs and humanity, so that what happened to Homer could never happen again. Their fervor was driven by Charles’ trauma of watching Homer get hacked by Vehement and then deactivate himself, along with their guilt from having participated in Jerry’s scheme.