As evident from Croc's "Meet the Trojan" comic the effects of said machine are not permanent (the effects only last about 2 weeks provided the power source isn't destroyed before-hand), and any and all victims DO have the chance to regain control of themselves and escape, though granted that's usually easily thwarted as another unit's almost always immediately ready to take over where the previous one left off.
But what if Amy, a victim of the Trojan Bot, managed to escape her capture, thanks to the help of a certain blue hedgehog? All should be fine and dandy, right? Back to normal? Status quo restored? Perhaps, BUT it was also stated in the comic that the nano metal which covers the victim's body (the thing that causes that wonderful metallic shine) is incredibly hard (if not impossible) to remove without proper tools. So what if that was the case? Amy escaped, but Tails wasn't able to remove the nano metal from her body? Now, every day, she has to live with the reminder of her previous fate, uncertain if she'll ever get to see her vibrant pink fur ever again.
Tragic? Quite. But spirit-breaking? Surprisingly, no! She won't let something like this stop her from living her life like she used to, albeit there may be the occasional awkward stare every now and then. If anything, though, this has now motivated Amy more than ever in the cause of taking down Dr. Eggman once and for all, to ensure that no one else suffers the same fate as her and any other rescued victims from this dreaded machine line ever again.
So not a good ending, but not a bad ending, either. As the title states, she's ill-fated... but motivated.
