Tony's episode opens on a shot of him and his new boyfriend sitting alongside his Mustang, which someone has vandalized as a warning not to testify. But Tony seems more concerned about his role as a witness for the school district, who will want him to talk about how Hannah blamed people for her problems and wanted revenge on her enemies. Such a testimony would force the Baker's lawyer to counter by making him look unreliable. Tony realizes that whether he tells the entire story or plays things coy, he'll ruin the Bakers' lives as well as his own.
On the stand, Liberty High's lawyer succeeds in twisting his words so that Hannah looks like a bully while the Bakers' lawyer brings out his anger management issues and his probation for assault charges. When pressed whether Hannah left written instructions for the cassettes, he lies and says that she did not. He then continues the lie by admitting he had no way of knowing Hannah's intentions and that he doesn't know why Hannah left him the tapes.
After the trial, he admits the truth to Hannah's mother telling her that Hannah left him the tapes because he owed her for protecting him from arrest during one of his assaults. The two bonded in that moment, and Hannah shared how she bullied a girl at her old school. Tony explains to Mrs. Baker that if he told the truth about why Hannah gave him the tapes, he'd also have to reveal her past. Basically, Tony didn't want that information exploited in court.