On Thursday, Yee addressed his immediate future. He now says he will withdraw his candidacy for California Secretary of State.
Yee is one of 26 people caught up in an alleged scheme that includes -- murder for hire and gun trafficking. There is also Raymond "Shrimp Boy" Chow a former gang member and Keith Jackson a former school board member in San Francisco.
Yee's political future is definitely uncertain. His attorney says no decision has been made about his Senate seat. But those who have seen the criminal complaint say the depth and breadth of the accusations is astounding.
The big fish in the federal case is Yee, but the initial target was Raymond Chow, who is known as "Shrimp Boy." He is a notorious Chinatown gangster with a criminal history that includes racketeering and drug crimes. Former FBI agent Rick Smith believes the agency's undercover operation was as tricky as infiltrating the mafia.
"They got somebody in the gang," Smith said. "And my understanding is there might have been some sort of induction ceremony. To do that here in Chinatown is a tremendous effort, takes a lot of hard work, and takes real expertise on the part of the undercover agent. "
The criminal complaint states that after the undercover agents gained Chow's confidence by laundering money, they expanded into drugs and then gun running.
That's when agents say Chow introduced them to Keith Jackson, a former San Francisco school board president who brought in Leland Yee.
San Francisco Mayor Ed Lee says he's looked at the 137 page complaint.
"They're like reading it from some kind of a mystery novel somebody had written," he said. "It was that strange to kinda see those allegations, but they were verified."
The FBI raided Yee's home, along with his office at the state Capitol Thursday.
The complaint states during a meeting at a San Francisco restaurant earlier this year, "Senator Yee told (an undercover FBI agent) that the arms dealer, 'has things that you guys want.' Senator Yee cautioned that doing business with people like the arms dealer was not easy and told (him) this was not a business for 'the faint of heart.'"
Yee's long political career is now in ruins with his attorney announcing Thursday the senator has ended his campaign for secretary of state.
"This is what he wanted to do in relation to that election for office given the circumstances of the federal case," said Yee's attorney Paul Demeester.
Some in Sacramento say Yee deserves his day in court. But there is also a growing chorus of calls for him to resign his Senate seat, like Senator Mark Leno, D-San Francisco.
"If he does not, the President Pro tem of the Senate has already announced that we will be voting on the floor tomorrow to suspend him," Leno said. "So Leland Yee will not be on the floor of the Senate ever again."
Others calling for Yee's resignation include California's senators in Washington -- Dianne Feinstein and Barbara Boxer.
In a statement, Sen. Boxer said, "I agree with state Senate President Pro Tem Darrell Steinberg that Leland Yee should immediately step down. If these allegations are true, they are beyond outrageous. "
Sen. Feinstein added in a statement, "The allegations against Senator Yee are shocking. It has become clear he has lost the confidence of his colleagues and for the good of his constituents should step down."
San Francisco Board of Supervisor's President David Chiu says while the allegations against Yee are shocking, there's an even bigger issue here. He says incidents like this are putting the public's trust in government at risk.
"We have to make sure that public officials are respecting the fact that when they take office, all of us are expected to abide by the highest ethical standards," he said. "And when something like this happens, as it has happened with three state senators in the past three months, it completely undermines the public's confidence in government."
As Chiu mentioned, two other state senators have been suspended. Both Ron Calderon and Rod Wright face felony charges and are on paid leave.
That means each of them receives their salary of more than $95,000 a year. If Yee goes on paid leave, the total amount picked up by taxpayers for the three senators facing charges is $285,873.
Since his arrest, the issue of how special interests groups influence lawmakers in Sacramento has resurfaced.
It seems Yee is no different from other politicians. Maplight is a website that collects and reports data on campaign contributions. Most of Yee's heavy donors are unions.
"The solution is just not kicking out the people who broke the law," said Daniel Newman with Maplight.org. "The solution is for all the current lawmakers to get behind money and politics reform."
Don Solem is a political consultant who worked in the state Senate with George Moscone 40 years ago. He talked about how lawmakers are tempted to take money from special interest groups because many are left owing a lot of money following a campaign race.
"Well, it's like a mortgage on your house," he said. "You have to pay the bill and I think public officials like other people are tempted to cross the line they shouldn't cross."
Yee had a $70,000 campaign debt from when he ran for the San Francisco mayoral race.