“He looked utterly surprised, like we were,” said Tyler Morse, a junior on the team who saw Mr. Scott escorted off the bus by the university’s head of public safety, into the car of F.B.I. agents.

On Monday, he was still wearing a blue hoodie when he was led handcuffed into United States District Court in Newark for a bail hearing. He was charged with one count of knowingly stealing an object of cultural heritage from a museum. He faces as much as 10 years in prison, if convicted.

Looking down as he was brought into the courtroom of Magistrate Madeline Cox Arleo, he twice replied, “Yes, ma’am,” when asked if he understood his rights and if he had retained a lawyer. The judge authorized an unsecured $50,000 bond, on the condition that he surrender his passport and agree to be supervised by pretrial services while remaining in the custody of his parents, who live in Longmeadow, Mass.

Drew University officials and students were shocked to learn that one of their own might be behind the loss of some of the university’s most prized possessions. Founded as a Methodist seminary in 1867, Drew has many important papers that shed light on the origins of the Methodist church and the Wesley brothers, who helped found it. It is also an official repository for the United Methodist Church itself.

According to federal prosecutors, Mr. Scott got a job in the archives in late October and was given a key to a storage room containing many documents considered too rare to share openly. Typical letters from John and Charles Wesley, for instance, can fetch $5,000 to $12,000 apiece on the market, according to the complaint.