During that year, Bonds completed his last season with the San Francisco Giants without the threat of a suspension and overtook baseball legend Henry Aaron to set the home run record.
"We pretty much were ready to go more than a year ago," said the former official, who spoke on condition of anonymity because the criminal case is pending.
"The question was what would happen to someone's career if they took this case and didn't win it," the former official said. "They wanted assurances" they would win a conviction.
The ex-FBI official said then-U.S. Atty. Kevin Ryan -- later among the U.S. attorneys fired in a controversial Justice Department housecleaning -- "was already in trouble politically" and reluctant to take on such a high-profile case unless it was ironclad.
Celebrity cases "had to be dead-bang," the former FBI official said, adding that investigators were confident they had sufficient evidence to support the charges. They also were hoping for cooperation from Bonds' personal trainer, who went to prison rather than testify in the case.
"Whenever you have an allegation like that, you never have just one source. We had several sources besides him, a variety of sources," the onetime FBI official said.
Calls to Ryan's private law office on Friday were not returned. He told the San Francisco Chronicle on Thursday that "the government has to make sure you have things lined up and that you've crossed your proverbial Ts and dotted your I's" in such cases.
A day after a federal grand jury here indicted baseball's new home run king, legal experts weighed in with a wide array of opinions on the strengths and weaknesses apparent so far in the government's case.
"It's a defensible case," said veteran defense attorney Michael Shapiro in New York. "Perjury cases turn on technicalities. A person who understood that is [former President] William Jefferson Clinton, who once famously said the definition of one of his answers depended on what the definition of the word 'is' is.
"Bonds is no Clinton, but prosecutors still have to prove what was going on in his mind when he said what he said."
San Francisco attorney Hugh Levine, a former county prosecutor who represented Bonds' former girlfriend, Kimberly Bell, when she appeared before the grand jury, said he was struck by the ambiguity of questions put to Bonds.
"My impression is the questions were posed poorly and imprecisely, and for a prosecutor trying to pin down a witness on perjury, [it was] a poor job. I thought the questions were loosey-goosey and informal almost to the point of being unprofessional," Levine said.
"Perjury is a crime that requires a high degree of precision," Levine said, adding that the questions that elicited the allegedly perjurious answers were something less than that.
"For example, using the word 'steroids' brings in imprecision because steroids are not illegal. . . . It is possible that the prosecution meant unlawful steroids, controlled steroids. That is what they have to make clear. . . . I would imagine the defense will use professors of linguistics [to testify] about words and multiple meanings."
Bell has said that Bonds told her he was using steroids but that she did not see him taking them. Levine said there is a strong circumstantial case to be made that Bonds was using performance-enhancing drugs, because his physique changed and because he had a connection through his trainer to the Bay Area Laboratory Co-Operative, or BALCO, a steroid distribution lab.
"That is one thing," said Levine. "Proving that those few sentences pulled out of his grand jury testimony are lies is another thing."
Former federal prosecutor Walt Brown, now a white-collar-crime defense attorney in the Bay Area, said he didn't question the questioning, but he wondered: "What's their proof [that Bonds lied]? What's their evidence?"