Cagalli receiving the Akatsuki, along with a recording from Uzumi, encouraging her to trust in her friends and loved ones. She then takes off to defend her homeland.
"Cagalli Yula Athha, Akatsuki, taking off!" The Lioness of Orb is back!
Uzumi's entire speech to Cagalli
Uzumi: Cagalli, should the day come when you have need of additional power consider this gift my answer to that need. There are many things I wasn't able to teach you myself. But if you have an open heart you can learn everything you will ever need from those around you, from those who love and support you. Therefore I can only give you what you see now before you. Power is what everyone makes of it. Foolish are those who hope for it in excess. Yet equally foolish are those who resent it for no reason. Think of it as a sword for protection if you need this now then take it. If it will help you walk the right path it is yours. However I had hoped the day would never come when This door would be opened. If it has been opened then these words may be in vain but my dear cagalli I wish you a long and happy life.
Athrun's open sorrow when The Freedom is destroyed, and Kira is presumed dead.
And some could argue that when Shinn comments he did it for Athrun could count. Though it only threw salt into the injury for Athrun.
On the flipside to the Freedom's destruction, Shin was able to get some closure for the deaths of his family and Stellar. And given the nightmare that Stellar called a life, it's nice that there was some retribution for her.
Episode 42: Kira still having complete trust in Athrun, in spite of the fact that Athrun was recently working for Zaft.
Phase 43, Neo to Murrue:
"I think that maybe... I know you. Yes... I know you. My body knows. My eyes, my ears, my arms... And that's why I couldn't just fly off. I think I know how hard it's been for you. It's been hard for me too. I would like... to stay right here, with you, by your side."
"Don't worry; I'll never leave you again... Murrue."HE'S BA-ACK!!! What lead up to this was quite possibly the biggest CMOA in the entire Gundam franchise, and this just seals the deal.
You know what? Shinn and Kira meeting face to face and becoming friends at the end of the Special Edition. Take that Hatedom—everybody wins.
Rau's interactions with Rey in the flashbacks. Durandal's father/son moments with Rey could also count.
At the end of the special edition we're treated to a scene of Kira and Lacus running up and embracing each other when they cross paths in one of the PLANTs. About half those present watch the two with warm, amused smiles, while a number of others go a bit slack-jawed, including Shinn and Luna. Manages to be funny and heartwarming at the same time.
Shinn's expression is rather noteworthy because he comes across as a lot more... relaxed than any other time in the series. Maybe he's finally found a bit of peace.
While the status of their relationship is a hotly debated subject, there are plenty of moments between Athrun and Cagalli during the series. There's him doing everything to protect her during the first episode, to comforting her when Shinn insults her father and him giving her an engagement ring. Cagalli also returns the favor plenty of times, by supporting Athrun's decision to go to the PLAN Ts and taking care of him after he's critically injured from his fight with Shinn and Rey. They also share a very emotional goodbye hug when she's forced to stay behind to help Orb.