The setting is inspired by Ghost in the Shell, but the game itself would be a lot closer to Shadowrun. Full-body cyborgs* exist, but are uncommon. The PC just so happens to be a full-body cyborg. Since he's an enforcer for a mobster, this comes in handy. One day he tries to screw over his boss, and gets put in a sexbot for his disloyalty. His first task is to shut up a mole for a rival mobster. It's possible to sell yourself to the other guy, but only if you do it right.
From here, you have a few options. Work for your boss and gradually regain his trust, or betray him and work for his rival. Each path has its own quests and storyline associated with it, as well as an ending.
Or, you could try to take down both bosses yourself. Might not want to do this right away, though. Keep doing jobs and making friends. Buy a safehouse. Once you're well-connected enough, you might just be able to pull off a mutiny. You can do it any time you want, but you might want to check if your friends have your back.
You upgrade by buying better bodies, armor, weapons, and firmware. You can also upgrade what you already have. Since your inventory is limited to what you could realistically carry, it's a good idea to invest in some built-in tools for your body. All the bodies you buy stay with you, and you pick which one you want to use for the mission. You can also arrange for a drop at a predetermined location, in case you need to swap during the mission.
*People with just a brain and some spine to call their own. Everything else is robotic.