Hunt for Traitors
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When Melinda May and Daisy Johnson escaped from the Triskelion, Alistair Fitz came to see Madame Hydra who had been severely injured in the process. While The Doctor was enraged at the sight of his lover in poor condition, Alistair told him that he had to lead HYDRA in her place while he led the chase for the rebels. He later received word that may and Johnson had been spotted and sent a team of HYDRA operatives to capture them. However, the operation failed since May and Johnson had reinforcements coming their way.
Alistair reported the rebels' escape to his son, who quickly got angered at him before Alistair chastised him, telling him that his reaction was unworthy of the education Alistair provided. The Doctor calmed down and told his father that he could not accept any failure, even from his father. Still willing to capture the fugitives, Alistair went to interrogate Holden Radcliffe who had been captured by HYDRA and could be a lead to the S.H.I.E.L.D. resistance. However, Radcliffe refused to cooperate, even after Alistair beated him up. All he could learn was that Radcliffe had communicated with Johnson while she was imprisoned in an adjacent cell, an information that he reported to his son. Alistair told The Doctor that Radcliffe was willing to die, to which The Doctor responded that they could give him a reason to live.
While reading at home, Alistair Fitz was confronted by Jemma Simmons, who threatened him with a gun. Simmons blamed Alistair for Leo Fitz's evil personality in the Framework, but Alistair kept telling that he was proud of his son's strong achievements. Simmons then forced Alistair to call his son and to ask him to come to the house alone. However, Alistair refused to obey and told his son that one of the subversives that HYDRA was looking for was with him. He overpowered Simmons and tried to neutralize her, but was eventually shot and killed by Simmons, who quickly fled.
Afterwards, Alistair's body was found by The Doctor and Holden Radcliffe, and the former swore to exact revenge on Simmons. This allowed Radcliffe to manipulate The Doctor into approaching a backdoor out of the Framework; he pretended to betray Simmons to The Doctor, but in reality, he intended to free Fitz from the Framework in order to atone for the mistakes he made as a result of his Darkhold corruption. Ultimately, Radcliffe's deceit worked, and he forced Fitz out of the Framework; satisfied that Fitz would "[get] to be his old self again", Radcliffe then apologized to Simmons for the horrific events in the Framework.