How it ended...
The last episode of Johnny Zero put Johnny right back where the show started...In jail.
After he set his australian friend up selling guns, he ran back to the club to get the fake passports that were made for him and his son so he could run. But he got picked up, and was told that his FBI friend was dead (killed in this episode). So now he had to go back into prison (undercover) to find out who ordered the hit. And once he did, the FBI agent that sent him in, double crossed him, and left him in there.