It is unusual for an investigation to go on this long and not lead to criminal charges, and that is far from the only unusual thing about this story.
Suspected of funneling campaign cash and kickbacks to friends and family, Perata had FBI agents searching his home, his office and his son's home.
"They raided his house, they raided his office, they served lots of subpoenas," Elliot Peters said.
Peters represents Perata's son Nick, who was also under investigation. He says San Francisco federal prosecutors decided a year ago not to go forward.
"And then the FBI agents weren't happy about that, they went up to Sacramento and shopped the case to different prosecutors in Sacramento and those prosecutors said, 'well gee, we'll take a look at this maybe we'll charge this case,' and that's something we thought was pretty outrageous," Peters said.
Peters believes it had to do with politics. And the politics here goes very high up. The letter from the Department of Justice announcing an end to the investigation is signed by the head of the DOJ's criminal division in Washington D.C.
"I'm just pleased that after five plus years, including my having to go before the grand jury in his proceedings, I'm glad that as of today the Justice Department, the Obama Justice Department have decided not to proceed," Former San Francisco Mayor Willie Brown said.
Brown says he understands being the subject of suspicion.
"It's a huge cloud, I went through that," Brown said.
When Brown was speaker of the assembly, the U.S. Attorney investigating corruption in Sacramento was George O'Connell.
O'Connell is now Perata's attorney and he provided ABC7 with a statement from Perata calling the DOJ decision "better late than never" and a "full vindication." Ultimately, Perata says he knew he had done nothing wrong and the truth would win.
Perata is now preparing to run for mayor of Oakland.
ABC7 political analyst Bruce Cain says Perata is the automatic front runner.
"He knows how to raise money, whatever campaign he runs will be extremely well funded; secondly, he will bring down a cadre of veterans from his previous campaigns and from Sacramento and we saw how much Willie Brown benefited from that in San Francisco," Cain said.