* Well, [[ItWasHisSled Phineas and Ferb find about Perry's secret identity.]] All fun and games except you know what that [[spoiler: almost]] ended up meaning.
* This movie manages to make [[spoiler:''StatusQuoIsGod'']] a tear jerker.
** "I love you, Pal."
** The fact that it does not end with mourning for those events, but Perry happily holds on to the memory of the best day ever.
* Phineas and Ferb meet their counterparts, and the alternate Phineas sees Perry and immediately hugs him, thinking he's ''their'' Perry, finally come home. When Phineas tells him that it's the wrong Perry...
-->'''Phineas-2:''' [[DoppelgangerGetsSameSentiment Wait...can I hold him a little longer?]]
** Even ''[[TheStoic Ferb]]'' (both of them, in fact) got teary-eyed at that part.
** Made all the more poignant when you remember how heartbroken our Phineas and Ferb were when Perry vanished for ''one day''. The alternate Phineas and Ferb have been without him for ''months'', at least.
* "I Walk Away". That is all.
* "I thought you couldn't spell 'platypus' without 'us'." Though, after a pause, Ferb makes a reply that makes this more of a funny moment.
* The final scene mostly [[Heartwarming/PhineasAndFerbTheMovieAcrossThe2ndDimension heartwarming]], but [[spoiler:the last [[http://images1.wikia.nocookie.net/__cb20110809162959/phineasandferb/images/2/22/PnF_AT2D_14.jpg photograph]], with Phineas and Perry sadly hugging...]] *sniff*
** Made even more upsetting when you remember that Phineas had been the most messed up over learning he was a secret agent.
* The scene where [[spoiler:all of Phineas and Ferb's friends and inventions arrive one by one in all their glory, fully ready for battle. It's not a scene where you'll shed tears of sadness, but some may shed tears of joy at the return of all the past inventions and the realization that something really, really awesome is about to happen ([[CrowningMomentOfAwesome which it does]]).]]
* When the main characters are all dangling off the side of the goozim cage, Perry is clearly in great anguish, knowing that if he fails, he will doom not only himself but also the four individuals who he cares for the most.