BOSTON — At the midmorning break in the trial of James (Whitey) Bulger, Patricia Donahue had a few choice words for Henry Brennan, one of the lawyers defending the crime boss against a sweeping slate of charges that include participation in the murder of her husband, Michael Donahue. She and her family approached him, and thanked him.

During the morning’s testimony, Mr. Brennan had pounded away at John Morris, the former F.B.I. supervisor who pleaded guilty to taking bribes from Mr. Bulger, but who has immunity from prosecution to testify against him. Under Mr. Brennan’s cross-examination, Mr. Morris described how he had learned that a Bulger associate, Edward Brian Halloran, was acting as an F.B.I. informant, and passed that information to John Connolly, Mr. Bulger’s corrupt F.B.I. handler. Mr. Halloran was later gunned down in a car along with Mr. Donahue, a bystander who happened to be giving him a ride home that night.

Mr. Morris denied that he had intentionally signed a “death warrant” for Mr. Halloran, as Mr. Brennan suggested, but at Mr. Brennan’s prompting, he looked directly at Ms. Donahue and her three sons and apologized.

“I don’t ask for your forgiveness, but I do want to express my sincere apology for things that I did and things that I didn’t do,” Mr. Morris said with tears in his eyes. “Not a day goes by that I haven’t prayed that God give you blessing and comfort for the pain that you’ve suffered.”