Warning: Spoilers Off applies to Heartwarming pages.
After seeing hints of it in several video games and other side content, Kira and Shinn are finally working together as trusted allies. Shinn also addresses Kira with nothing but respect, showing how touched he was by Kira's offer at the end of SEED Destiny.
The film is pretty much the culmination of Shinn’s character arc, having finally found a cause worth fighting for with Compass alongside a close circle of companions that give him much needed emotional support, particularly from Luna, and is generally the happiest and healthiest he’s been in a long time. Furthermore, as a sign of how much Kira’s influence has rubbed off of him, Shinn has also adopted his own code of using non-lethal force whenever possible. Overall, he has come a long way from the angry and vengeful young man that he was during the events of SEED Destiny.
If you look closely during the battle in Africa, you'll see that there are people hiding behind the Immortal Justice's shield, which was stuck in the ground at the time. This means that Shinn deliberately gave up some of his equipment for the sake of civilians who had failed to evacuate in time. This short scene alone is proof of how Shinn had finally obtained what he'd always wanted; not the power to destroy, but the power to protect.
Hearing Shinn take off, announcing "Shinn Asuka, Justice!" is a very pleasant surprise. In a direct repudiation of Durandal's view that Shinn was nothing more than a tool, a soldier guided by his Impulses and Destiny, dictated by his DNA... he now pilots the Justice. It means he is finally free to prove he is so much more than the simple sum of his parts.
Moreover, Kira has specifically chosen Shinn to pilot the Immortal Justice in Athrun's stead. Despite their history in the Second War, Kira trusts Shinn with the other Gundam used by Compass.
The fact that ZAFT and the Atlantic Federation were able to join forces with Orb in forming COMPASS as a means of keeping the fragile peace between Earth and the PLANTs, in spite of the lingering animosity from the Alliance-PLANT wars, shows that Siegel Clyne's dream of peaceful co-existence and cooperation between Coordinators and Naturals is very much possible. As if to underscore this, Blue Cosmos is a shadow of its former self here thanks to the majority of the Atlantic Federation finally refusing to tolerate their genocidal tendencies anymore. They have very little forces left by the time of this film, having to use 105 Daggers instead of Dagger Ls or Windams. Gone are the days when they could do stuff like just waltz into any Earth Alliance base and demand access to their mobile suits, most of the Earth nations aren't having that anymore.
As racist as the Blue Cosmos members are, Kira Yamato refuses to let them die to his own vengeful allies, no matter how justified they are. Kira really does want to end the fighting so everyone can live in peace.
Kira covering Lacus with a blanket after coming home late and finding her asleep on the couch from having made dinner for the both of them. Then, when Kira falls asleep, Lacus takes the blanket Kira put on her and covers him with the blanket.
According to the Novella Escape for Two, Lacus likes making dinner for Kira, but she always makes way too much food. So she and Kira often give their extra food to the COMPASS staff, who not only appreciate their generosity, but also find the food delicious.
Kira and Lacus go on a little picnic date. Between their respective duties, it's nice to see the two young peacekeepers get some respite and just enjoy a romantic outing with one another.
Mu, despite losing his Murasame's head and left arm, comes back to rescue Murrue right before the nuke hits.
After Athrun punches the daylights out of Kira, it gets Kira to admit that he wants to be with Lacus, and Athrun, seeing that Kira is ready to go back to the fighting, helps him up.
Shinn was so shocked at Athrun casually punching Kira in the face that he immediately jumps into Kira's defense.
Hilda was one of the most loyal Clyne Faction soldiers in Seed Destiny while Shinn was one of the most loyal soldiers to Durandal who wanted to destroy the Three Ships Alliance. Despite their history, Hilda holds no grudges against Shinn and even actively looks out for him from saving him from the Black Knights to stopping him from entering a fist-fight between Kira and Athrun.
A Freeze-Frame Bonus of Shinn's belongings in Lunamaria's room when she thought he died when the Immortal Justice was destroyed shows that he still has Mayu's phone, confirming that it was not destroyed alongside the Minerva in Seed Destiny.
Shinn and Kira's reactions to seeing the Destiny Spec II and the Strike Freedom Type II is a mixture of heartwarming and awesome, but especially for Shinn. The tone that he gives out shows is a mixture of meeting an old friend, ready to join his friend in kicking ass, and wanting to save the world. Unlike Shinn seeing the original Destiny Gundam which was played for horror as a new machine to help Shinn get his revenge on Orb under Durandal's orders, everyone knows this time that Shinn will be using the Destiny Gundam for good.
The fact that the Destiny was upgraded into its Spec II at Orb under Cagalli's orders implies that she has forgiven Shinn when he attacked Orb in SEED Destiny in that same Gundam which also nearly killed Cagalli in her Akatsuki. Likewise, this implies Shinn has also managed to move past his hatred for Orb and how he blamed the Athhas for the death of his family.
Kira giving the order to Shinn, showing that he's ready to trust in his allies.
Kira: Shinn, I'm leaving [the defense of] the Millennium to you.
Shinn: [smiling an energetic grin] Got it!
When Murrue Ramius hijacks the Millennium in order to fight the Foundation, Alexei Konoe immediately offers Murrue the captain's chair. She accepts, and lets him become her XO.
Captain Alexei Konoe and Lt. Albert Heinlein in general. We only meet them here, and they don't have a lot of scenes, but it's made all too apparent that they are loyal and steadfast allies of our heroes. Our first scene with them after the opening battle, Konoe asks if Kira isn't going to go home earlier so he can spend time with Lacus, showing he values their relationship. They don't doubt in the slightest that their comrades survived the Foundation's ambush and will be back soon enough. While moored at ORB, when Murrue and Kira try to take the bridge hostage while in infiltration gear, they instantly knew it was them, Heinlein even musing that they took two minutes longer than he expected, and Konoe sighs that they didn't need the "ominous" gear to simply take over the ship. Hell, earlier, when Heinlein alerts that they're being hacked, Konoe merely sighs and slumps, which we realize is because he's probably thinking "They could have just walked up to us and asked nicely, not go through any hijacking attempt". So too are the rest of the Millennium crew, including former Minerva bridge crew Arthur Trine and Abbey Windsor. And that's before you learn from side materials that Heinlein has been the designer of every Freedom and Justice and a Clyne loyalist and inside man since the start, even if we only saw him now.
The Orb Military immediately rushes in to help Kira and the others make the Millennium hijacking look genuine, including firing live rounds at the ship, with one of the ship captains who served Todaka in the previous war, former First Lieutenant Amagi, swearing they will help Kira get back into space.
Unlike the incompetent Seirans, Cagalli was properly prepared for the Foundation declaration of war, already getting the people evacuated and into safety, including using Astray units to pick up buses and cars to evacuate people quickly and having the Kusanagi already on standby. She is NOT letting what happened to Orb in the previous two wars happen again.
It is small but the fact that Miriallia and Sai are within the Orb military and they show up with Cagalli means that unlike at the beginning of Destiny, she is not alone anymore and has her friends with her.
During the preparation, Cagalli not only prays to her father to protect the people, but also to Kira. Kira then answers Cagalli's prayers, forming a plan by taunting Aura so that the latter would get distracted trying to kill him, buying Cagalli extra time. It shows how far the siblings trust each other, and how Cagalli values her family.
The novelization of the movie has Cagalli's inner thoughts to Orphée's declaration of war with him forcing the Destiny Plan on Earth and preaching the use of the Requiem on nations not complying to the Foundation's demands, all in the name of Lacus Clyne. Cagalli doesn't buy for one second that her friend wanted that, feeling that Orphée has insulted everything Lacus stood for. This only strenghtens Cagalli's resolve against the Foundation but it also shows how much Cagalli values her friendship with Lacus.
Cagalli (thinking inwardly): "How dare you use Lacus's name! How dare you invoke it for such an ultimatum!"
Athrun immediately thinking of Nicol when seeing Mirage Colloid being used.
Murrue has named one of their tactics after Natarle Badgiruel, indicating that she still respects her former comrade. This is especially heartwarming when she likely believed that Natarle's last moment alive was (supposedly) killing Mu by ordering the Dominion to fire at the Archangel.
Kira and Lacus reuniting at the climax of the movie. Ingrid realizes the two are genuinely in love by the way they hug and the fact that both robot birds they have fly with each other.
Lacus' love for Kira is just this in general. Despite being captured by Foundation and having a literal genetic match in Orphee, Lacus keeps resisting his advances because of her love for Kira. No matter what tactics Orphee used, from words to thoughts synchronization to even Attempted Rape, Lacus' love for Kira remains steadfast and immovable. It's especially heartwarming because things seemed far less certain in the first half of the movie.
Similarly, after Kira had agonized about his relationship with Lacus in the first half of the movie, having Kira practically shouts his love for Lacus to Orphee in the Final Battle (of which he is losing), even calling it his greatest weapon, is both amazing and heartwarming, especially when you remember that this is the first time Kira said it out loud in the series, finally turning them both into an Official Couple. To seal the Power of Love, the Strike Freedom Type II does its signature Full Burst mode while a remix of Tobe! Freedom! plays in the background. It really shows how having Lacus to fight for brings out a side that hasn't been seen much since SEED.
Kira: "I still have one weapon left!"
Orphee: "What weapon?!"
Kira: [Does a full burst attack and activates SEED Mode] Lacus' love!!
Even death will not separate Stella and Shinn this time. Stella's spirit now resides in Shinn's mind that she immediately jumps to protect him from the Black Knight's mind control by assuming a monstrous form to kick all of them out of Shinn's psyche.
Even though Yzak and Dearka had to kill Hari Jagannath in the end, Yzak and Dearka tries to reason with the ZAFT coup forces to surrender because they don't want to end lives for no reason.
During the duel with Agnes and Lunamaria, Agnes says that Lunamaria has been badly influenced all because she dates Shinn calls him a loser. Luna shoots her down verbally and physically with the Impulse's machine guns, telling her that she's Shinn's girlfriend because she likes him compared to Agnes who only dates men for their specs.
While mostly funny, the fact that Athrun thought of Cagalli naked actually protected him from Shura's attack, and that Athrun has confidence that Cagalli will not let him die in his duel against Shura by entrusting remote control to her.
The novel implies that the "shameless thought" was a memory, as Shura sees not only what's implied to be Cagalli having sex with Athrun from the latter's point of view, but also all the happy moments Athrun and Cagalli experienced together and everything that Athrun likes about Cagalli, from things like dates, the perfume Cagalli uses, and even the way her skin feels.
The fact the ending implies that Cagalli forgave Athrun for thinking of her naked, even after her initial anger.
Athrun already having his Infinite Justice Type II (which was very likely upgraded at Orb alongside the other Gundams) with him before the others received them, implied that Cagalli has entrusted it to him, making this trust mutual.
Lunamaria picking up Agnes at the end of the battle, like how Athrun picked up Shinn and Luna in Destiny. Despite having every justifiable reason to dislike Agnes, Lunamaria decides to be the bigger woman and show compassion to someone who doesn't deserve it, showing how Athrun and Kira's values rubbed off on her.
During the ending credits, the warm smiles Athrun and Cagalli give each other help convey how much they mean to each other. Athrun shows Cagalli that he is still wearing the Haumea amulet she gave him in SEED, and she responds by showing him that she started wearing the engagement ring he gave her in SEED Destiny again (albeit as a necklace as opposed to on her finger), implying she's finally ready to marry him.
The two Cavalier Units carrying Athrun and Cagalli's respective Mobile Suits are even seen flying alongside each other, implying they are all going home at Orb togethernote Presumably Meyrin and Kisaka's commando in Unit 1 used by Athrun. Miriallia, Sai and Chandra in Unit 2 used by Cagalli..
The final scene of the movie, and possibly the Cosmic Era as a whole, is Kira and Lacus sharing a sexual moment on a beach together, affirming their love for each other with a kiss. After surviving multiple wars, personal tragedies, and an ordeal that nearly tore their relationship apart, the two have well and truly earned their happy ending at last.
Several of the Gundams are quite sweet in concept. The Mighty Strike Freedom is the personification of Kira and Lacus' bond. The Duel Blitz and the Lightning Buster were built as a cooperation effort between ZAFT and the Earth Alliance, showing how the world powers want to establish peace. The Destiny Spec II has a darker-gray color and a different beam rifle as if replicating Rey's Legend, and the Duel Blitz's name and weapons say it all. Shinn and Yzak never forgot their fallen friends, even after all this time. The second volume of the novel states that Yuri Amalfi, Nicol's father was involved with remodeling the machines which hints that he made the Duel Blitz in honor of Nicol. It also doubles as entrusting the Duel Blitz to Yzak, despite him giving Nicol a hard time early in SEED.
The Escape for Two novella offers a brief respite to Athrun and Cagalli :
What is at the beginning a serious meeting quickly transformed into a makeshift date between the two in a restaurant at Orb, a place the blonde Natural liked to go. Just Athrun and Cagalli enjoying a meal, chatting, happily bantering and laughing together like a normal couple. Even if they are not openly affectionate to each other, it is clear they still enjoyed each other company. Special mention to how jovial Cagalli was during the meal, since becoming the Chief Representative of Orb in SEED Destiny, she rarely smiles or laughs like this. But at that moment, Cagalli is just a normal girl who was eager to let her boyfriend try the dishes she ordered for them. Cagalli was also cooking a cabbage dish for Athrun, knowing that he liked cabbage, the Coordinator happily tastes the food his girlfriend gives him if he can offer her the break she wanted. And also Athrun actually laughs with Cagalli.
The main reason why Athrun "kidnaps" Cagalli ? She wanted to be away from her bodyguards for just a brief moment and them having replaced the staff and the customers of the restaurant she liked with Orb bodyguards ruined that little pleasure of her (Cagalli was understandably angry at them for that) and the chief bodyguard insisted to bring her back home calling her "selfish", objectifying Cagalli. This triggers Athrun so much that he decided to get Cagalli away from them, wanting to fulfill her wishes, even for just a moment, thinking she is still a person with desires and a heart. Cagalli was happy to go along with her boyfriend
When the Black Knights attempt to use their mind powers on Shinn, he lambasts them for underestimating him, thinking that they can inflict a darkness greater than what he has gone through prior. Considering Shinn has moved on from his previous angry, rage filled self in Destiny, and that he's more happy and fulfilled. As well that he know knows Kira trusts him, this really speaks of how much Shinn has improved mentally. Not only that, but it shows that Shinn's previously maligned character faults became his greatest weapon. His troubles weren't for naught, they made him stronger in the end when channeled more productively and controlled as opposed to the reckless berserker he became later in Destiny.
When Yzak, Dearka, and Shiho meet up with Clyne loyalists on the Eternal, no surprise that Eileen Canaver is among them, but who is the surprise is the woman in a purple ZAFT uniform next to her: Ezalia Joule. Last time we saw her, she was Patrick Zala's Number Two among the radicals and Canaver herself led a squad to arrest her. It is good to know that of the anti-Natural radicals of the first war, one of them was able to reevaluate herself, turn over a new leaf, and now actually fight alongside her own son and his crew as one of the good guys. She even takes the time to eye Shiho as a potential partner for her son, to both their annoyance.
