Following the defeat of Team Rocket, Proton stays on with the group, but his cruel actions and general animosity towards the remaining members put him at odds with the rest of the team. However, because he was a good agent, he was allowed to remain. In this time period between when Giovanni left and Silver took the reins, the sort of de-facto leader was Petrel – Archer having left the team to find a new path in Sinnoh and Ariana having been arrested. As such, Petrel saw himself responsible for ensuring Proton didn’t do anything too reckless or awful that would reflect poorly on the team or cause trouble.

During this time period, Proton was in a sort of fling/hook-up/rivals-with-benefits relationship with Domino. Proton had previously been dating Will, but after Team Rocket’s first defeat, Will, along with Karen and a number of other members defected from the team. Proton was angry and upset that his boyfriend had ‘betrayed him’ like that and was taking out his frustration with numerous ‘rebound’ relationships that were purely physical and generally ended quickly and explosively. (In truth, Proton and Will’s relationship was very unhealthy and Will realized this with Karen’s help, choosing to leave Team Rocket not just because he no longer agreed with the Team’s actions, but also to protect his and Proton’s unborn child, Perry, who Proton didn’t want.)

During his relationship with Domino, Proton discovers he accidentally became pregnant. While he initially doesn’t plan on keeping the baby, having no interest in being a father, he eventually realizes he could use the kid as leverage against his rival and decides to keep them. After Atlas is born, however, Domino shows no interest in the kid and tells Proton he was silly for thinking she would care, brushing him off and essentially breaking up with him. Furious, Proton now saw Atlas as nothing but a burden and a waste of space, not even able to serve his supposed purpose. When Petrel heard rumors that Proton had had a son, he was immediately concerned for the child’s well-being, with good reason, as when he visits Proton’s apartment to check in, he finds Proton nowhere to be found and Atlas very ill and almost dying of neglect, not having been properly fed or taken care of by his father.

Petrel takes Atlas into his care, luckily able to get him the medical treatment he needs and saving his life, and officially exiles Proton from Team Rocket for his actions, as this had gone way too far. Proton is pissed, but he leaves without looking back, figuring that the Team was holding him back anyways. Following this, Petrel takes it upon himself to raise Atlas as best he can, feeling responsible for what happened since he didn’t think to investigate Proton sooner. When Atlas is still a baby, Silver returns and decides to take over and reform Team Rocket and Petrel is happy to hand the leadership to his old boss’ son. After this, Atlas is raised mostly by Petrel, but other Team Rocket agents along with Silver help raise him as well, so Atlas is essentially raised by the new Team Rocket as a whole. For legal purposes, though, Petrel is his guardian and adoptive father.