She was captured by the Covenant and is the object of the Human Error quest. She is the supposed daughter of Old Man Stockton, a prominent caravan merchant from Bunker Hill and a member of the Railroad. If the Sole Survivor asks him if his daughter might be a synth, he can give varying answers. One possibility is that he doesn't give a clear answer but states that she is his daughter.
Alternatively, if Old Man Stockton knows the Sole Survivor as a member of the Railroad from having completed Boston After Dark he will confirm her identity as a memory wiped synth and reveal the Institute took his daughter away and replaced her with the current one that is present, keeping her as she is the closest thing to his daughter.
She can be pickpocketed of her synth component, giving a player the rare ability to determine her nature before deciding her fate as it is possible to run past the guards and directly to Amelia before proceeding. Her nature as a synth is verified by her guardian, Old Man Stockton.
If you rescue her from the compound without activating the quest Human Error, she will not leave her cell even if opened and all the guards are killed. She just repeats, "I am not a synth" and "I just want all this to end" in the cell for the rest of her existence.