Simon Riley used to smell like apples, specifically granny smith. It pissed off his dad, as everything he seemed to do did, and it cause a lot of problems between them. To rectify that he covered his scent constantly which is not healthy but if it meant he had to sleep with a few less bruises and a ringing in his ears than so be it.
Because he smothered his scent it started to change. It was more tart and when uncovered, leaked profusely. But that was ok. Sure his glands itched but it kept him safe.
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Lt. Ghost smells like dirt and rot. After the events of Mexico and Roba his scent changed. Once one goes through a deeply traumatic event, especially for longer periods of time, the distress and environment can change ones scent. And that is precisely what had happend. His scent is much weaker now, a result of scratching at his glands to protect himself from others harming him, but once worked up anyone close enough can smell the earths woody smell coming off of him in waves, rotting from the inside.
Ghost hasn't been comforted in years, not really, he won't allow himself that, so it's hard to tell if the rot is from new hormones or old ones. Most are disgusted by it and due to his military standing he still covers his scent more often than not. It adds to his cover, his new identity.
But when he's happy and relaxed, a shadow of his old scent peaks through, just a little citrus under the musk.