Aha, I find it kind of sad that this is the only thing I've come up with that has any substance to it. Sorry it's so short!
X had been the only one allowed to witness the sealing.
None of the others even knew about it. It was Zero's decision and Zero's decision alone. He had made such a decision with a heavy heart, though he was relieved. If it meant he had to leave to bring peace, so be it. But that didn't lessen the impact for X any. If anything the resignation that the Reploid displayed had only made things worse. Their last days had come and pass quickly, not giving either of them a chance to think or regret their actions. Things were prepared dates were set, a place was found. It wasn't glorious, unfitting to be his place of rest. Underneath the main HQ's building was a chamber that used to belong to Sigma himself. He used to store his most important documents and items there, so it seemed only fitting that the most important of them all would find themselves among the former Maverick Hunter's leader's most important data and belongings.
It was simply Zero and X. Nobody more, and nobody less. X begged him, expression strained and wrought with worry. He didn't have to do this, there were other ways, he whispered. But the deed was done and life was exchanged for peace, a cold metal shell behind solid glass. X was pleading even after the case sealed and Zero's words ceased.
He cried, he fell to the floor and told him everything he never did. He told him every little thing he loved about him, that he regretted never letting him know, that he had let the blonde sacrifice himself so many times for his sake. X fell to the floor and he cried. He cried into the night, long after his tear ducts ran dry and his voice was hoarse and edged with static and garbled messes of interference. He cried when he was found by Axl, who had gone through a wild goose chase to even know he was there. He cried as he told him what had happened, how his pleas had been in vain.
But since then, there was not a single tear that has left his eye. He involved himself in his work more and more, his personality that was once so kind now twisted and maimed to the point that whether you could even call him X was debatable. He no longer hesitated, not on the battlefield and not prosecuting others if he was ordered to do so.
The others were worried, but Axl was the only one who could even dream of getting through to him. He was lonely, occupied only be his goal and the aching inside his chest that shouldn't have been real-couldn't have been, surely. He silently damned his creator for making him so kind, so /human/. His worrying and sorrow were what made him unique, and what also made him untouchable.
But no matter how bad he felt, he always made time to visit Zero. Whether they were separated by glass or he was simply a pile of wires on the engineer's table, he would find him. Nobody dared to try and hide his location, lest they have to deal with the bitter anger that X had managed to produce and thrive on since Zero's sealing. He would talk to the sleeping Reploid, voice soft and emotional. Then, and only then, would he cry.
It could never amount to the floodgates of when he first began to spiral, but rather they fell silently and without prompting. It had become a natural response to the sight of him, to the softness of his skin and the golden halo of hair that spun from his helmet.
And some days still it became too much. He would retreat to him room and refuse to answer to any call. He would cradle the handle of a familiar Sabre close to his chest, limbs tangled in sheets and mind spinning and whirling too much to even hear call from the outside hall. Alia, Axl, Palette, even Signas tried to get him. It ranged from quiet pleas to stern commands, but none of them reached his ears.
He was afraid of what would happen when it did. Would they lose all hope to discover that he spent his time leaving red marks in his hands from gripping the handle of the Z-Sabre? To see him fumbling to come up with a response to basic questions, his blankets and sheets dragged into the common room of his dorm with him? It was too much for even him. Not that much was, anymore. He had since lost track of what exactly he held dear, a scale becoming a pile of memories and emotions that melted together until he couldn't discern anything from one another. How he wished he could break this vicious cycle, but the one thing that could make him soar on pure hope and love was the one thing that sent him spiraling out of control.
His name was X, and he was alone.