Flame recoils back in pain, after having a bright light shined directly into his eyes while they were accustomed to the dark. He then sees the gun and realizes what Wily just did. Flame's pupils dilate as he realizes that Wily has just injeted him with a reprogramming signal.
Wily looks at him with a smirk, feeling satisfied with his work, he now has a new tool.
However.
Since Flame is in fact still part human, the reprogramming does not do its job properly, or fully, for that matter, ad Flame begins to scream in pain as his organic components begin to conflict with his machine body. His Human mind conflicting with his mechanical brain
"AAAAHHHH! AAAHHHHRRRRGGGHHH! TH-THIS PAIIIIN- I CANT- AAAAHHHHHH!!!"
Flame falls to the ground in a convulsing sparking heap, veins popping out all over his face, his nose bleeding, and his tears bloody from the vessels popping.
Reprogramming a cyborg usually does not work. Due to part of the person being human, the human part conflicts with the rest, since living tissue cannot be reprogrammed since it is not machine. usually, the more machine and less human one contains, the easier the reprogramming. Flame is such a cyborg... However, he is not a common cyborg either. he has his EX core, which has partial immunity to all reprogramming and viruses due to it being linked directly to Flame's nervous system. Since the immunity is only partial, it still gets partially corrupted, which in turn, causes Flame even more pain...
Not that Wily could know that though...
Wily seems to actually be somewhat taken aback by it all, not expecting a simple reprogramming job to be so messy. he didnt even know that robots could bleed... "Ze robots in zis vorld mast be pretty advanced..." Wily thinks to himself as he watches Flame.
"AAAAAAHHHHHH!!! I-I-I CANT! I CANT T-AKE IIIIIT... I- AAAAHHHHH!"