* Cubone reuniting with its mother. Also doubles as a TearJerker.
** When Red uses the Silph Scope, it is finally revealed why Marowak was chasing people away. She was trying to ''protect them'', because Team Rocket was ''still occupying the tower''. A common belief before this was she had become embittered towards humanity--turns out the opposite was true.
--> '''Marowak:''' *Upon having its true form uncovered* Get out! Leave this place! You shouldn't get close to them!
* [[spoiler: Giovanni vowing to end Team Rocket and atone for his crimes after his Gym battle with Red. The scene where he remembers how he felt about Pokemon as a child is even more heartwarming for viewers who grew up with the original games.]]
--> [[spoiler:'''Giovanni:''' There was a time where I, like this boy, was obsessed with Pokemon. Those were different times. Where business and money didn't come before Pokemon. I feel like I've become that boy from long ago.]]
** The best part? Turns out Giovanni's very first Pokémon was a [[spoiler: [[NotSoDifferent Charmander]].]]
* [[spoiler: When Red's Mega Charizard X attacks Mewtwo, Red has a brief moment where he sees his old Charmander fighting in Mega Charizard X's place, and you realize just how long they've been together and how much they've been through together.]]
** Red's dialogue from the scene really nails it home.
---> '''Red:''' [[spoiler: Charmander, we've come so far together...]]
* The fact that Pokemon Origins ''even exists at all''. Great tribute to the 90's kids who played the games from the start.