The alternate ending starts off in the past where Spike and Vienna went to talk alone outside.
"What do you think they are talking about?" asked Patty.
"I don't know." said Magenta going to the window to look.
"Um...so Spike...you see...I really..." Spike said as Vienna smiled and a hand on her hip.
"Uh...uhhh...NO!"
"What?"
"I can't do it! Damn it I love Magenta!"
"Oh come now. You can't possibly." said Vienna leaning in for a kiss. Spike slapped her, and quickly went back inside. Vienna shrugged and went back inside.
"What was that?" asked Magenta.
"We had a fight." Patty said. She then looked at Patty and Noah. "Sorry guys."
Just then a time warp surrounded the two. Noah looked at Patty, and she quickly faded away to nothing. Noah got sent back to his own time.
And so the time warp created another scenario. it created a new universe, a new dimension caused by a somewhat butterfly effect. Riff Raff, Magenta, and Frank were warped back to the earth castle. They had no idea where their children were. Ansalong, Ricky, Bert, Farley, Cosmo and Nation were warped back to Denton studios with their memories wiped. Brad and Janet were warped back to their houses. Their memories were wiped as well. The warp had done nothing to Eddie, he was still in the freezer. After much searching and research, Riff Raff sadly deduced that all his children were wiped clean from the face of existence, neither appearing in heaven or hell. There was no possible way to ever bring them back. After Riff Raff told the news to Magenta and Columbia, they both broke down and cried in his arms. Riff Raff cried as well. And soon, life at the castle was depressing.
As for Vienna, she destroyed all of Transylvania in the other dimension, but the galaxy was unharmed in this new one. Frank soon went more and more insane, and forcefully had sex with any visitors in the castle. Riff Raff and Magenta wanted more than anything to gor back to Transexual, but Frank would punish them if they tried to use the teleporter. The only possible way to return was to beam up the castle. Frank kept a close eye on them at all times.
After a few years, Frank went completely insane, and with Satan no longer interested in Frank, he wanted to create a better man, and devoted all his time doing so, and so project Rocky Horror was put into full swing. Frank even used part of Eddie's frozen brain. Every night, either Riff Raff, Magenta, or Columbia was forced to sleep with him every night. Any refusals resulted in a whipping, and a raping. Riff Raff suffered severe depressions, especially the nights when his sister was sleeping with Frank. As for Magenta, she began suffering from mental disorders. Riff Raff was always there to try to help her out through the pain. Columbia went slightly insane, pretending to be oblivious to the changes of lifestyle, and being happy and perky, in a disturbing way.
And it was also decided that the annual Transylvanian convention be held at the castle. The ball room was being heavily decorated by everyone. Frank threatened to kill Riff Raff, Magenta, or Columbia if they confessed the way he treats them to the Transylvanians. But unknown to all of them, a certain couples car has broken down, and they were on there way to the castle right now...