1)When her body was brought in for Project Lazarus there wasn't enough viable/useable material still on her body to be restored, therefore they came up with something well outside the box: use what materials they had as well as the tech they'd planned to use repairing Shepard to make a smaller body, then essentially download her brain into her new body when they were done. This change of plans also meant Miranda never even considers the 'brain chip' as she assumes she could easily control a girl she could hold in her hands.
2)Shepard is whammied by a Collector weapon, whether it's during a battle or due to a malfunction when they bring it back to the Normandy the end result is the same
3)Anything else
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