Nanite is a new proto-type AI. The scientists of the Galactic Council were going to scrap Nanite after it showed too much emotion and didn’t wish to pin point targets for them, which it was programmed for. Out of luck, Quinn showed up right as they were about to destroy Nanite. We will never know why Quinn stopped them, and took Nanite, but they have been inseparable ever since.
Even Quinn didn’t know how much Nanite would learn and how close they would become. Quinn would tell you Nanite is not just a robot; Nanite is a friend. There is no distinction between the robot side and the emotional almost organic side…
Quinn has always wondered why Nanite was so emotional/organic. One day he decided to ask Nanite what you remembered about the day you were made. Nanite thought, and painful flashes of different things popped in and out and Nanite didn’t want to think about it anymore. Quinn felt bad for putting Nanite through that, but as well he didn’t forget and wanted to figure out the puzzle. Even though Nanite struggled with wanting to figure this out, it didn’t matter because this is when the Admiral called in Quinn to go after Viper.