Early in the 2014 football season, a Nike representative entered the Penn State athletic trainer’s office and confronted the football team’s two doctors and head trainer.

The representative ran down a list of players, including the star quarterback, whose socks and shoes had recently been taped over to help stabilize previous injuries. The tape covered the Nike swoosh, and the representative wanted it stopped, court testimony showed.

Soon, the coach, James Franklin, began to interfere, requiring the trainer to provide a list of players who needed their ankles taped over their shoes, along with an explanation. The episode was just one instance that troubled Scott Lynch, the head team doctor, who had begun to feel that in the face of pressure from the coach and administrators, he was the only line of defense for the athletes. He complained to supervisors about the coach’s meddling with medical decisions. Ultimately, Dr. Lynch was removed from his position. Then he sued.

Last year a Pennsylvania jury awarded Dr. Lynch $5.25 million in damages for wrongful termination. The trial offered a rare glimpse into how a high-profile college football team handled decisions around injuries — and revealed the pressure on trainers and doctors to greenlight students to get back on the field, despite reservations.

“College sports are broken, and I think they’re beyond repair,” Dr. Lynch said in an interview. “There’s way too much money that’s getting in the way of people making good decisions. Nobody’s protecting the athletes.”