Carl ran to the museum. He didn't realize how horrible everything was without, well, evil. As stupid as that sounded, it made perfect sense in context. He pushed several people out of his way to get in screaming "LET ME IN! THE FATE OF THE WORLD AS WE KNOW IT - or, rather, I know it - IS AT STAKE!". He jumped into the time machine and pulled the lever.
"Hey! You can't..." a museum security guard began to tell Carl.
"...do that." he finished after Carl had gone to the past.
Carl was about ready to fix Doofenshmirtz's life for the better, when a second Carl showed up.
"No! Don't make his life better!" Carl told Carl.
"Why not? It'll prevent him from being evil, won't it?" Carl asked Carl.
"Well... yes, but --" Carl explained to Carl
"Then what's the problem?" Carl asked Carl. All of a sudden, a third Carl showed up.
"We need to get out of here, you handsome fellas" Carl told Carl and Carl. "The universe is in grave danger..."
"Hold on, I just need to make Dr. Doofenshmirtz's life better, then we can go and do all this 'getting out' you want to do." Carl answered. One by one, more Carls began to come in. Eventually, there were more Carls than residents of Gimmelshtump.
"WAIT!" Carl yelled to the mob of Carls "I think we should all just go back to our own time!" All the Carls agreed with him, and they got in their respective time machines (or maybe some other Carl's time machine, they can't tell the difference).
Back in the future...
"Where's Carl? He was supposed to be here 20 minutes ago!" Major Monogram complained. Suddenly, a mob of Carls ran in and smothered him. With his dying breath, he yelled "CARL! YOU'RE FIIIIIIIIIIRRRRRREEEEEEDDDD!!!"