In the final season of Breaking Bad, things really got bad between Jesse (Aaron Paul) and Walt (Bryan Cranston) as the former realized he needed to move away from Heisenberg. Many innocent lives were caught in the crossfire of their meth business, and Jesse got an opportunity to leave Albuquerque with his fixer to start a new life. However, this actually led to Saul Goodman's biggest mistake -- one that would break them forever and change their lives in a massive way.
Jesse couldn't handle the fact that kids were dying and Walt didn't care. All that mattered was keeping the Heisenberg façade up and cooking meth, so on Walt's advice, Jesse wanted to head to Alaska with a new identity in "Confessions." However, when the fixer's van pulled up and he checked his pocket for his cigarettes, Jesse realized Huell, Saul's aide, had picked him.
He rushed back to Saul's office where he began beating the lawyer. Saul thought it was for Huell picking the weed Jesse had on him, but it ran much deeper. Jesse eventually held Saul at gunpoint and got him to spill the details on one of the show's biggest mysteries: what happened to the ricin cigarette. Jesse was supposed to use it to kill Gus a while back, and when he and Walt fell out, he thought Walt stole it and used the ricin to poison Brock.
It turned out this wasn't the case, but Jesse now realized that even if the cigarette wasn't used, Huell did pick him. Saul, bleeding and scared, admitted that they stole the cigarette for Walt but never knew what it would be used for. They were complicit, though, and Jesse couldn't forgive them because while Brock barely survived, he threw away his love for Andrea, Brock's mom, and kept his distance as he felt it'd be dangerous for them.
In reality, Walt poisoned Brock using a flower, not the ricin, but Jesse was still pissed that his suspicions and mistrust were confirmed. This shattered Jesse as he thought Saul and Huell were his guys, but instead, they inadvertently destroyed his last shot at true love, happiness and having his own family. Granted, they didn't know Walt's intentions, but still, it left Jesse enraged and heading to Walt's home. After all, Walt convinced him that Gus stole the cigarette out of his locker to poison Brock in revenge, and later, Jesse thought maybe he lost it.
All these mind games had Jesse trying to set Walt's home afire but he was stopped by Hank (Walt's brother-in-law), who had just figured out Walt's secret. This changed the dynamic of the final few episodes as Jesse then worked with Hank and Gomez to get the DEA evidence to bring Walt down.
Sadly, Heisenberg was a step ahead and used Todd's crew in this civil war, which ended with the agents getting killed and Jesse being enslaved by Todd's neo-Nazis. Walt was cast aside and the crumbling of the empire all came from Saul and Huell invading Jesse's privacy -- twice.