Cubone reuniting with its mother. Also doubles as a Tear Jerker.
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!
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.
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 Charmander.
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: Charmander, you've really grown strong, haven't you? We've come a long way...
The fact that Pokemon Origins even exists at all. Great tribute to the 90's kids who played the games from the start.