This is how I wanted it to end, though I love the original ending, it would be good to have one that wasn't down to chance like that, eg. why did shrapnel only hit penny? Anyway, here it is.
Disclaimer: I do not own Dr. Horrible's Sing-Along Blog
Dr Horrible stood, aiming his death ray at a frozen and entirely defenceless Captain Hammer.
'Here goes no mercy'
Then there was a whining down sound from the freeze ray, and he flicked his eyes back to it desperately, that wasn't a good sound. Captain hammer could unfreeze in a matter of seconds.
Oh god, here goes. He squeezed his eyes closed and pulled the trigger. He had needed more time to get it together, but he had none. Why didn't his plans ever go hitchless.
The freeze ray's whirr finished, and there was a thud in front of him. His heart thrust against his chest hard, as if making a desperate attempt to leave, before returning to its normal-if slightly fast-rhythm.
He cracked his eyes open to see captain hammer crumpled pitifully, and not moving. His mouth turned up briefly. Here lay everything he dreamed of, yet it seemed to easy and he was left with a bitter taste in his mouth. That was not elegant, though he made the best of it with the freeze ray entrance. At least Penny didn't see. He brought the death ray down to his side and turned round to see the people peering from chairs and anything they could find to cower behind. Stun was written on their faces. Things were as unmoving as if he'd used the freeze ray on them. Then his focus shifted. A flash of red hair vanished through a door. Was it Penny? He somehow couldn't find the will to find out.
He pulled his goggles over his eyes and began to walk confidently across the room. He stumbled and fell, landing on his face.
'Damn goggles, can't even see through them' He pulled them off.
Journalists started asking questions as they saw an opportunity, but he just heaved himself up and left, with as much dignity as he could muster.
He turned on his camera, pointing it at himself. A wicked smile formed and crept slowly up his face.
"I guess you saw the news, Captain Hammer, dead." His smile stretched slightly as if he'd bit into something unpleasant, "a triumph if there ever was one. They got pictures of me flat on my face, but a success nonetheless." He reached to the table next to him and grabbed a letter, shoving it into the camera. "But HERE's what the news won't have told you. I, am officially in the league. You heard right, the Evil League of Evil has accepted me, Dr Horrible, into their midst. Finally." He paused, looking to the side for no discernable reason. "I obviously haven't seen Penny yet, but tomorrow's Wednesday, and I'm sure she'll be somewhat pleased to see me. And with Captain Cheeseball out of the way she may finally be mine, so yeah, see you after that."
Billy walked into The Coin Wash, hopeful. No sign of Penny, but there was a bag left on her dry cleaner. He smiled uncertainly and walked over to it, carefully peering in. In it were two frozen yoghurts and spoons, and a note that simply read 'Goodbye.' He took out the note and barely began to tear it before getting a paper cut and dropping it to the floor.
Billy walked away, pulling his revised goggles from his pocket and over his eyes, and vanished. All that was left of Billy was left on the floor of the laundromat, a bag of laundry, and a slightly torn note on the floor, with a message on the other side.
That evening Dr Horrible arrived at the evil league of evil to quite a welcome party, having donned his revised black gloves, red lab coat and goggles. He had no need for Billy.