Perry the Platypus in "the Digital World" is the 3rd episode of New Super Flynn-Fletcher Bros! It is the Bonus Perry Stage!
This is after Doof sucks the Tri-State Area into Irving's game. For the full scoop, click here. Now, Perry can't talk in the real world, not even in the Digital World, but he can communicate with the other agents with a special "animal language" that we translated to English.
(Agent C, the chicken): I'm scared.
(Agent T, the turkey): I'm more scared than you! Tomorrow's the day everyone looks for Thanksgiving turkeys!
Perry is just waking up from a coma, and he's seeing the other agents hovering over him.
(Perry): Ugh. What happened?
(Pinky): Doof actually won. He sucked us all into this video game and it put you in a coma.
(Agent L): Snap out of it you guys. We've gotta defeat Doofenshmirtz!
(Pinky): Now let's find Doofenshmirtz Evil Inc.
It's right behind them.
(Perry, turning around): Hey, guys! It's right here!
They go in, only to find Doofenshmirtz with Poofenplotz (Poof) and the Regurgitator.
(Doof): Ah, Perry the Platypus...
(Poof): And Pinky the Chihuahua...
(Regurgitator): And Larry the Lemur...
(Doof): Anyway, you're all so unexpected! And by unexpected I mean... unexpected. How'd you even get in here with my force field? Wait, I know. Norm forgot to turn it on, didn't he?
Perry and the agents can't talk to people.
(Perry): Growly noise thingy.
(Doof): Enough! Now I will tell you the rest of my plan! Now that everyone in the Tri-State Area is "playing" this game, I will hack it, with my Hack-the-Game-Inator hooked up to my Game-Database-Inator! I will make it so everyone follows me! Now to enter the right code...
Perry escapes and jumps at the self-destruct button.
(Regurgitator): Look out! He's after the self-destruct button!
He pushes the button, which makes everyone leave the Digital World.
THE END of the bonus section. Again, for the full story, click here.