Found this idea on AO3, I just had to write it.
Characters still aren't mine.
The blue alien wasn't the only thing Coulson found in the guest house. He saw something else, a file. A file on him. Everything they did to him in great detail. Unlike the medical file which only contained the information on how they brought him back to life, but what they changed in his memories. Tahiti was only the tip of the iceberg.
He hid the file under his bulletproof vest as he and Garrett ran out of the guest house, and back to the plane. Coulson read the file after May's visit. He couldn't tell her what he found, not yet. She didn't need that burden now.
Coulson opened the folder slowly, mentally preparing himself for what he was about to know. The first half of the page described the procedure on how they changed his memories. The bottom half was the description of the Tahiti implant. On the second page, the description of the 'Mobile Command Unit desire.'
"Agent Coulson will be reassigned to a Mobile Command Unit, seeing that he will not be satisfied with a job in administration. In the MCU he will also be closely monitored, and it will decide his future out in the field. Also, to make the transition easier for him."
In the next page, he felt his heart stop on the heading. "The Cellist." He started reading frantically.
"The Cellist implant, is the result for the need that Agent Philip J. Coulson's relationship within the agency with Agent Melinda May to not restart. It is of his best interest to refocus that outside of the agency, and onto a mythical person he can never contact. Thus, keeping him objective when on missions with Agent May, who will be assigned with him.
The cellist character was chosen, since Agent Melinda May also plays for the orchestra: cello, second chair. Also, Agent Coulson's past descriptions of her to the Avengers as a cellist, and will make it easier for doctors to manipulate Agent Coulson's memories.
In his memories' the image of Agent May was replaced by the image of a fictional woman, and all of his strong feelings for Agent May should be transferred to her.
In the next medical examination of Agent Melinda May, a less drastic memory alteration process also took place unknown to the said agent. Removing the memories of her and Agent Coulson's romantic relationship from her mind. Even her memories about Portland, and her cello skills need to be removed. To be replaced by her normal comings, and goings in administration. She will only remember their distant past, in the academy, missions together, and the trust between them which the agency needs.
Agent Melinda May shall be briefed, before she is contacted by Agent Coulson himself. This has been approved by Director Fury. Level 10 Clearance."
Coulson felt the tears sting his eyes. When he flipped through the next pages, he saw the file on him and May, pictures of them together, looks like it was in Portland, that was real. A smile on both his and May's faces when they were having dinner in 'the Richmond', her playing the cello as part of an orchestra with him smiling in the crowd, and just the looks of contentment when they were walking through the park, with their hands intertwined.
He slammed the file shut. Coulson couldn't take anymore lies. Fury altered his memories of May, and destroyed hers. He had to tell her. He just had to, but the thought of putting her in danger overwhelmed him. Coulson wouldn't know what to do if May got hurt now.
He had to find Fury.
After a couple of days, he still had no idea where Fury could be. He just met up with Agent Sitwell when he got a call from May, saying Lady Sif has arrived in the middle of the desert.
"...speared it with her double-bladed sword. It was pretty badass." He looked at her, and did his best to hide the way he felt.
"She says she needs SHIELD to help her find someone. You up for this?" May just looked at him like she always has before.
"I'm fine." He tells her, and was walking towards the stairs.
"Fine doesn't look like this. Not on you." May looks so worried.
"Whatever's bothering you, I'm here." He wanted to tell her so badly, but he needs to do this, for her safety.
"I know." He continued to walk down the stairs.
"I'll run diagnostics. See how much damage we're dealing with." He looked at her, saw the bruise forming under her eye, most probably cause by Ward, who was under Lorelei's spell.
"How much are you dealing with?" Coulson was concerned about her, the plane could wait. He saw her tense even though her back was to him, clearly thinking of a way to make him think that she was alright.
"He didn't break anything. So..." She gave him a small smile, in trying to show that she was fine.
"That's not what I meant. You should talk to him. Hash things out." Even though he is now aware of his and May's past relationship, she was with Ward now, and he could see that she cared for the younger agent.
"You should take your own advice. You've been sitting on something, since the guest house." May came closer putting a hand on his arm, she could tell that Coulson was deep in thought. May put her hands on his arms, in trying to comfort him.
"If not with me, then with Skye. She deserves to know what you saw in there." Coulson let out a breath when May finally went to the cockpit. If she didn't leave soon, he might have cracked and told her what really happened in there. He almost put the woman he loves in danger.
He still took her advice though, and went to the medical pod to talk to Skye.
"I trust them, but we need to protect them from this." Coulson didn't tell her about the file. That was something he needed to figure out for himself, but he told Skye everything else, and they were going to go after them together.
"Agent Melinda May. Update log 93. He knows. I repeat. Coulson knows." May slammed the phone back to its spot, and breathed out, clearly frustrated.
Unknown to everyone, May kept a personal record of her life. She could still remember how she felt when she realized that SHIELD messed with her head. They made her forget about her time with Coulson, they almost erased the trace of her love for him. But the didn't succeed. May needed to protect Coulson. From Centipede, the Clairvoyant, even Fury. That's why she keeps up this charade with Director Fury, to make him think that May was still on his side, seems like it worked.
FIN.