Early in the movie, we see the first hint of Makoto's kindness when he helps Fuuka pick up her books.
While this may seem like a stock Pet the Dog act, this is especially effective when you think about Makoto's characterization. At this point, he is pretty much an Extreme Doormat who only really acts when ordered to. And the fact that he's willing to take the time to actually help this girl he's never met before out - and without anybody, not even said girl, asking him or ordering him to do so, that says a lot about his character.
During the Shadow Priestess boss fight, when Junpei tries making a reckless charge against her, Makoto pulls him away. He then summons Jack Frost, who absorbs the Priestess's ice attack. Makoto then lets Junpei get the final blow against the Shadow, which affirms their bond. Better when you remember Jack Frost is of the Magician Arcana.
The Fuuka and Natsuki scene during the Empress and Emperor Shadow battle, when Fuuka rushes down to check on her (avoiding the attacks by the Shadows), followed by Natsuki apologizing for her cruelty to Fuuka. This prompts Fuuka to summon her Persona.
Then at the end, we see Fuuka returning to school, and though Natsuki doesn't remember the above moment, she offers to listen to Fuuka if she has problems. Outside, Makoto, Junpei and Yukari are watching them and we see Makoto smile (normally) for the first time, surprising the latter two. They smile in return.
Midsummer Knight's Dream
The heart-to-heart talk Yukari and Makoto have at the beach, when she discovers that her father was responsible for the explosion at Port Island. He comforts her telling her that her joining SEES wasn't for naught, and that he does appreciate both her and everyone's friendship.
The summer festival at the shrine, when Makoto, Aegis, Ken and Shinjiro all watch the fireworks together from Ken's secret place. Ken recounting how he can smile again after years of loneliness thanks to everyone is really heartwarming.
Ken's admiration of Shinjiro in general is adorable, especially compared to the game where he spent a great deal of their time together holding a grudge against him for killing his mother. Here though, he doesn't remember that yet, so he gets to know Shinjiro's good side first.
Aigis telling a depressed Makoto that she will be with him as long as he lives. This is followed by Makoto embracing her.
In a matter similar to a Social Link, Ryoji helps Makoto (who has been gloom since the previous movie) to cheer up.
Chidori's coldness towards Junpei is toned down in the movie compared to the video game; she opens up to him more easily, begins looking forward to the time they spend together, and shows noteworthy horror when Junpei gets shot by Takaya.
Winter of Rebirth
After being told that the world will end before spring, the group slowly distant themselves. However, as they think about the people they love and lost, the group slowly regain their will to live and resolve to end the Dark Hour once and for all.
Around the same time, Makoto gives Elizabeth a tour around the city. As they converse, Makoto remembers his experience over the year and the friends he had made. Realizing that he isn't alone for the first time since the incident ten years ago, Makoto vows that he will not let the world end.