I wrote this after surfing around on the Phineas and Ferb wiki. On Perry1914's and Doof1914's pages, it says that they are both presumed dead after the Juatchadoon temple collapse. They were still in the main chamber when the walls and floor began to crack. They weren't in the river boat with the others. Ohio and Rhode Island don't even pause to consider whether or not they could have made it out in time.
Even though they would be dead anyway, being almost one hundred years old, I couldn't let any Perry perish. Not even a counterpart from a century ago. That's why I wrote this... a scenario where Perry1914 and Doof1914 survive.
Perry dodged the swipes of his opponent with skill as smooth as silk. Doofenshmirtz took another swing at him with the corn cobs he was holding in each of his hands.
"Ah ha! You just wait 'till I connect with one of these. Then you'll wish you'd never been corn! Get it? 'cuz it rhymes with..." Doofenshmirtz lamely attempted at a clever spat.
Perry, being a platypus, didn't reply. He wouldn't have anyway. It was too pitiful of a pun to be considered a worthy opponent for his own wit.
"Hey, what's with the fez anyway? We're not even in Egypt!" the evil archaeologist continued as Perry flipped out of his reach.
"Yeah, that didn't really make sense. But Monogram insisted. I think he might have been confused by all of the pyramids," Perry thought to himself.
Fortunately, the fez was equipped with some special technology. Perry pulled the tassel of the fez, triggering a small set of copter blades that rose out of the hat and lifted it from his head. Underneath, his regular brown fedora was revealed.
The fez hovered in the air for a moment before darting toward Doofenshmirtz. A mechanical grasper lowered from inside it and grabbed the amulet that Doofenshmirtz was wearing around his neck. Then it ascended out of the temple.
Doofenshmirtz watched his hard earned goal fly away out of his reach, once again.
"You're a real spoil sport, you know that?" He said to the platypus agent.
Perry glared stoically at him. They sat in silence for a few moments before the ground suddenly began to shake. The walls started to crack. Large chunks of ceiling began raining down on the two foes. Perry looked around nervously.
"Oh, terrific. The temple is falling apart! Are you happy? Probably my face will melt now, and for what?" Doofenshmirtz ranted.
"What does your face have to do with anything?" Perry asked, although Doofenshmirtz couldn't understand him.
The entire temple was rent in pieces and both of the fedora wearing mammals ran as fast as they could to the exit.* Perry knew they wouldn't make it. They would be buried in rubble. He hoped those other archaeologists had made it to safety.
Suddenly a huge wall of water crashed through the chasm. Perry and Doofenshmirtz barely had time to draw in deep breaths before they were hit with the wave. It almost knocked the breath out of Perry, and he saw bubbles escaping from Doofenshmirtz's mouth as he was knocked against a rock that had previously been a part of the Juatchadoon temple walls. He was unconscious, and unless Perry did something quick, he would drown.
The anthropomorphic platypus had not come through unscathed either. He was bruised all over from the impact of the water and fought to remain awake. He managed to get his brain to function properly after a couple of seconds and grabbed the archaeologist by the collar of his coat. Then he paddled as hard as he could for the surface.
It was such a long way up. Perry's lungs were about to burst. Although he was semi-aquatic, platypuses actually couldn't hold their breaths for much longer than humans. He could see the wavering sunlight, but the edges of his vision were getting red. He continued to move his free arm weakly, and even his tail and hind legs, but his chest was about to burst and he felt his grip on Doofenshmirtz weaken. He was still slowly rising in the water as his eyes began to droop heavily and his teeth clenched with effort to keep his breath. Finally, he couldn't hold it any longer and a cloud of bubbles escaped his bill. The last thing he remembered was the horrible pain in his chest as water began to fill the vacuum...
Something was on his mouth. Perry tried, but failed to opened his eyes. His chest still hurt and felt heavy and water logged. His mouth was free, and he tried to draw a breath, but he couldn't.
He reflexively rolled over as bile rose in his throat. He gagged out so much water, he was surprised that his small body could possibly fit so much. Perry barely had time to draw a small breath before he began vomiting again.
Tears streamed from his eyes. He was suffocating all over again. Just when he was sure he was about to pass out once more, his airways cleared up and his lungs drew in huge gasps of oxygen. He coughed a few times and gasped some more. He managed to get his eyelids to separate enough to tell through his blurry vision that he was surrounded by green. Sunlight shone in dappled patterns on the ground, but before Perry could get his full bearings, he slipped back into unconsciousness.
When he awoke for the second time, Perry groaned in pain. His throat was swollen, dry, and sore. His lungs ached. His limbs were too heavy to move and he had an awful headache.
He opened his eyes and glanced around. Someone was moving to his right, but he couldn't see them clearly enough to tell what they were doing. He made a chattery-growly noise to get their attention. A strong, olive skinned man with black hair and a somewhat flat face turned to glance over his shoulder at the splayed monotreme.
He said something, but Perry wasn't sure if his ears weren't working right, or if the man was speaking a different language. The man must have read the confusion on his face, because he tried again, this time in English.
"English comprendo? You speaking?" He asked.
Perry blinked as he recognized the heavy South American accent and realized that the man had originally been speaking Spanish.
"Well, I don't actually speak at all, but I communicate with English, yes," Perry nodded.**
"You I finding in water with friend," the man said while gesturing to another body behind him. It was the evil archaeologist, Doofenshmirtz.
"He's not my friend," Perry spat.
"Enemigo?" The man interpreted.
"Yeah, 'enemigo'. As soon as I can get him back to the town, he's going to prison." Perry finally found enough strength in his arms to sit up a little.
"Drink," The man said, handing him a canteen of water.
It was fresh and cool, unlike the salty wave that had filled his lungs earlier. It hurt to swallow because his throat was still as rough as sandpaper, but it made him feel better. He was beginning to get dehydrated.
"You being a strange thing. I never was seeing A animal like you in this jungle."
"Only a few people know I exist. My species is exclusive to Australia," Perry shrugged.
The man accepted back his canteen and turned back to Doofenshmirtz who was beginning to stir. It was strange, seeing him without his hat. Perry realized that his own fedora was missing, not to mention his fez. He looked around, but they were nowhere in sight. Glancing back at the two humans, Perry crept away into the jungle.
He made his way toward the "river". He figured the canal had been created by the destruction of the Juatchadoon temple. Scanning the water for his fedora, the platypus began to pad along the crack in the earth.
Miraculously, he saw it, caught on a branch at the edge of the water. He hopped in and paddled over to it. After shoving the soggy hat onto his head, he glided back toward shore. He crawled out onto the bank on all fours and lied down to rest again. He was still lacking energy after almost drowning.
After a few deep breaths, Perry continued to make his way back toward the humans. He had to make sure that Doofenshmirtz was brought to justice at last.
The End
So that's how Doofenshmritz and Perry survive. I don't really know how the dancers got out. I hope they left after Ohio distracted the Corn Colossus.
*What? Humans are mammals too! I couldn't really find anything else they had in common
**You see what I did there? Just in case you didn't, or you did and thought you might have to correct me, I just put a comma at the end of that dialog before saying, "Perry nodded". Normally, you're not supposed to do that, because nodding is something you do while you are speaking, not actually the speaking itself; So you would put a period. For example:
"I am very impressed." John clapped.
But here, let me defend my use of a comma. Animals communicate through more than just vocal sounds. They use a lot of body language and scent too. I am interpreting Perry's communication to the clarity of English so you can get more inside his head. Not every time Perry says something does he chatter. That only makes up a portion of his vocabulary. Humans communicate through body language too, but probably not as consciously as animals do.