A Watcher, Amy's first field assignment was to Watch Morgan Walker, whose then cover was a modeling agent, but was in fact a dangerous immortal, who ran a sex trafficking ring, and had a penchant for casually murdering the mortal women in his life.
Amy suspected Joe Dawson had pulled strings to get her assigned to the field prior to her classmates, though she was only tenth in her class. When she confronted him about it, she revealed that she knew Joe and her mother, Laura, had had a relationship and he was her biological father.
While Amy reported Walker's latest murder to Joe, Walker ran into Methos, whom he knew as Dr. Benjamin Adams, and challenged him. Methos refused and walked away. Methos then tried to enlist Joe's help in providing information about Walker, but Joe rejected him outright, angry at Methos for having disappeared without word months earlier. Methos accused him of hypocrisy and Joe told him to get out.
When Amy was discovered by Walker, her cover story didn't stand up to his scrutiny, and he took her prisoner. In yet another exposure of the Watcher network, he went through her notes and recordings to discover Joe Dawson's name. In hopes of more information, he ordered Joe followed and picked up.
With Amy's disappearance, Joe turned to Methos since Amy was Watching the man Methos was interested in. Methos, understandably, was reluctant to help Joe, until Morgan's men start shooting at them. Methos took a bullet for Joe, and the two fled from Walker's goons. Walker was told of the man who came back from the dead who was travling with Joe and the pursuit continued.Once cornered, Methos took out Walker's goons, while Joe got a call from Walker who proposed trading Amy for Dr Adams. Joe agreed, though guilt ridden. Eventually, he came clean with Methos and the two men met Walker together. Walker threatened to shoot Amy, but Joe responded with, "You shoot her, I will shoot you. And I will make sure the doctor takes your head." Methos took the long postponed challenge as Joe and Amy moved to safety.
Amy asked Joe why he had never been in her life, he admitted he and her mother had thought it was best for him to stay away. He offered to give the fatherhood thing a shot and Amy softened to him and implied 'someday' she would be open to a relationship.
Amy was re-assigned as an apprentice Researcher on the Methos Chronicle under Dr. Amy Zoll. Although, during her rescue, Joe made a point of not revealing his ally's name, calling him the Doctor in front of her, it is unlikely in the extreme that Amy had any idea the immortal involved was Methos.