Danny Fenton/Phantom was captured by the GIW and the blinded him only for Danny to be saved by Young Justice. Warning Torture.
He literally just transformed in front of you five minutes ago!
This paragraph is a very long run on sentence. Try separating it into smaller sentences. This is not the first time you have done this. I think you story would be so much better if you fixed that problem. Other than that I love the story line.
It ticks me off that NOBODY notices when he's overshadowed. It's not like his eyes are BLOOD RED OR ANYTHING.
I started singing Hold Up by Beyonce in my head when he said this
So far, your pacing has been a little fast. Try adding more details to bring the story to life. You have a really awesome idea here and it would so much better if you just reread it and fixed it up a little bit.
As far as the run on sentence thing goes, I would recommend reading your paragraphs out loud. If it feels natural to stop or pause, then add a period or comma. Just try not to use too many commas, I've seen people do that too. :) Love the story concept so far, good job!