I think it's because he's gone rogue, and he's on a deluded quest to get cortana back while evading capture by the UNSC. He's cloaked so no one recognises him.
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Why does the UNSC want to capture him, did I miss something?
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My theory is that Cortanas death has made him extremely depressed and he's decided to go on a lone crusade to find her. But the UNSC think his mental state could be a threat to people so they're trying to find him. Also, maybe the Librarians augmentations have done something to him which makes him dangerous.