AN: This is my first, and probably only, fanfic. I'm not a creative writer. But I've really felt there was a lot missing between the final episode of Season 1 and the first episode of Season 2. It seems to me that at least a couple months or more have passed, and there had to have been some serious stuff going on to get Jane and the team to where they are at the beginning of Redemption. Here's my take on what probably occurred in between. I've hypothesized a little bit, but I think it's plausible within the canon. Many thanks to Kathi-Ann for betaing, for her insightful comments and suggestions on the story, and for discussion back and forth beforehand that led me to this.
In the immediate moments and hours after the shooting, he was numb. It didn't really hit him. Sure, he'd thrown the rifle away in horror, like a poisonous snake; yes, he'd been filled with hopelessness as Hardy expired in front of him, whispering those last enigmatic words; he'd felt despair and frustration as his only possible link to Red John evaporated… But he hadn't really had a choice. If he hadn't acted on pure, almost animal instinct when Hardy pointed his gun at Lisbon, not only would she have died, but probably others too before it all ended. There really had been no option, given that the rifle was at hand. As the hours dragged on before they could return Maya to her home – yet another family torn asunder by Red John – he had come to terms with it, or so he thought. Lisbon had given him new feelings to ponder, down in that cellar. All in all, the worst had been averted, and he was genuinely happy that Maya had been saved. As he meandered through a nearby orange grove and slowly peeled an orange, he really believed he had come through it ok.
But as the days and weeks passed, it hit him. He'd killed a man. He'd taken a life. Hardy had been a monster who had worked with the ultimate monster, a man who had helped kidnap two young women and kill one, who had threatened him at gunpoint, who had threatened Lisbon in very horrible terms. But still, Patrick had taken another person's life. Never mind that he intended to exact his vengeance on Red John much more viciously than the easy death that Hardy got. The reality of it sank in and started to affect his very sanity. It became more important than ever to find Red John, to assuage his guilt, however misplaced, over killing Hardy.
As normal procedure, the CBI had wanted him to undergo counseling, just as they did for the agents who took a life in the line of duty, who'd undergone such stress – especially those for whom it was the first or second time, and especially for someone like him who had never even been trained for the possibility. He resisted, of course. He hated the idea of doctors, especially psychologists who would try to get into his head much as he tried to get into the heads of others. But they made it clear to him that he couldn't go on consulting for the CBI unless he did. He finally, grudgingly, agreed to see the shrink. He could feel himself becoming unhinged again, and knew that if he ever wanted to stay sane enough to complete his, well, his life's mission, to find Red John, he needed the help. Plus he needed the access to the CBI, so there was a practical reason for it too.
But too soon, before he really was helped, he decided he had had enough, so just as he had at the mental hospital, he faked his way through the sessions until the doctor signed off on him. Far from healed, however, he was spinning out of control. Before he had killed Hardy, he could set Red John aside long enough to work with the team coherently, but now his fixation on finding Red John grew into a panicked frenzy that consumed his very being. He lost his focus, his edge, his abilities. He started making stupid errors, missing things. The last straw was the case in the department store, where his actions resulted in the death of the suspect.
Finally, Minelli had had enough, and determined that a fresh set of perspectives was necessary. Not only to relieve the stress on Lisbon and Jane and their team, but hopefully to finally catch the monster who had destroyed so many lives, and was destroying the SCU team in front of his eyes. There was only one thing left for Minelli to do. He knew it would hurt Jane and Lisbon more than anything, but it needed to be done. The Red John case needed to be given to someone else. Even if it was the hardest thing he ever had to do.