When Kazuki returns to the island he tells Soushi that although he listened to what he said and fought, he didn't understand that Soushi himself was suffering along with the rest of them. This causes Soushi to break down into tears and finally agree to cross with Kazuki again.
Every single one of the Fafner pilots plus Soushi standing up during Maya's trial and declaring that they were the ones who falsified her data. Doubles as a Crowning Moment of Awesome.
Made even more so when you realise that Soushi - Mr By the Book - was the instigator, being the only one aside from the adult and Tsubaki who knew beforehand.
Sakura and Kenji sharing a moment, with Sakura confirming that she returns his feelings. This swerves into Nightmare Fuel territory; immediately after the scene she collapses to the ground as her mind is assimilated.
Heaven and Earth
It's small but when Fumihiko and his crew try to find Misao's ship and it doesn't show up on the radar everyone except him start doubting. Why doesn't he? Because Soushi gave them this data so something is guaranteed to be there. It's kinda sweet to see that he trusts Soushi completely, even when he has no concrete proof it's actually from him.
Kazuki and Soushi's reunion in the movie. This is topped off by Kazuki's eyesight being restored and having Soushi be the first thing he sees again.
Kazuki: I can see... I can see you!
Soushi: Thank you, Kazuki. For protecting the island... My place to come home to.
Kazuki: Welcome home.
Kazuki's character development comes across as this. In the original series he was so tormented by what he had done to Soushi that he wished he could just disappear. Compare that to now, where he greatest wish is to live and protect the people he cares about. It also doubles as a Tear Jerker, given the context of the show.
While throughout the entirety of the first season Soushi and Kazuki could barely stand to look at each other, they're now comfortable enough with each other to lie side-by-side on a beach and stargaze.
In the original series, when Soushi is revealed to be an incredibly socially awkwarddork, Kazuki can only give a baffled "You're really awkward, aren't you?" By Exodus it's turned into a term of endearment. He drops it a couple of times and looks like he's melting on the inside each time. Soushi might be a dork, but he's Kazuki's dork.
Soushi telling Kazuki to have good dreams when he takes a nap on their trip to India, and asking him whether he slept well once he wakes up.
Reo reassuring Mimika that the growth that replaced her eye isn't weird or gross by showing her how his own SDP (holes growing in his body) has worsened. Seeing the two of them laugh and joke around like the kids they are is adorable, especially after the time they've both spent BSODing about their SDPs.
After Sui finally snaps and ask his parents to get over his sister Sanae's death as his mother insists to launch the Second L Plan, so that the lives lost from the First doesn't go in vain in Episode 17, they finally find their error of ways and Kaburagi becomes a loving family like any others from the second half.
While the situation itself is nothing less than grim, Soushi jumping in front of Kazuki to protect him when an assassin of the New UN tries to shoot him, without a moments hesitation, still counts.
Kenji and Sakura deciding to get married in Episode 19. Even more so when we consider the fact that Kiyomi is the only one left among their parents......but she still lives long enough to see the two getting married.
When all is said and done, Chocolat is the authority on whether Kouyo is actually the real Kouyo.
A Fridge moment, but Kazuki, Soushi, Maya, Kouyo, Kenji and Sakura become proper adults is one.
And a meta fridge-heartwarming moment only seen when watching the episode live: In the commercial for the BD release of the original TV series, footages of Shuoko and Mamoru are being used. It's a good reminder to the audiences that they are still not forgotten.
Crosses into Tear Jerker, but at the end of Exodus Soushi finally becomes one with the Festum... only to be reborn like the Alvis Cores. Seeing the Two Years Later epilogue with reborn Soushi and Kazuki on Watatsumijima really takes the biscuit.