Officials at the Second Mile, the charity for at-risk children that Sandusky founded and that prosecutors say he used to target victims, reported that several years of the organization’s records were missing and had perhaps been stolen. The missing files, investigators worry, may limit their ability to determine if Sandusky used charity resources — expense accounts, travel, gifts — to recruit new victims, or even buy their silence, according to two people with knowledge of the case.

And in 2002, after McQueary had reported what he had seen to the university’s senior officials, those officials not only never told the police, but they also never even informed the university’s top lawyer. That lawyer, Wendell Courtney, said in an interview this week that he would have been duty bound to report to law enforcement officials any allegations of inappropriate conduct toward children by Sandusky.

Most disturbingly, investigators continued to identify possible victims — young men who had been boys when Sandusky befriended them through his foundation for troubled youngsters.

Those young men were not eager to tell their stories, the two people with knowledge of the case said. The young men were not convinced that the attorney general’s office had the will to go after a case that could rewrite the storied history of the university’s football program. And they asked: If the case went forward, who would believe them over a revered figure like Jerry Sandusky?

It was a question investigators had asked themselves. But with McQueary, they had what they regarded as an impartial witness, and one from within the ranks of Penn State itself.

Accusation, but No Charge

Penn State was shaken by the Nov. 5 arrest of Sandusky, the indictment of two university officials on charges that they had perjured themselves and failed to report Sandusky’s alleged crimes, and the ouster of both Paterno and the university’s president, Graham B. Spanier.

But back in 2009, when the case first landed in the office of the attorney general, no one knew where it would lead. The mother of a Clinton County, Pa., freshman called the local high school to report that her son had been sexually assaulted by Sandusky. Sandusky was barred from the school, where he had served as a volunteer coach, and the matter was reported to the authorities.