Breaking into the supposedly-impenetrable Leiston Fortress.
The Martial Arts tournament. You've heard about it from various NPCs since Chapter 1, now you're in it to win it! And THEN it turns out a bunch of familiar faces are also involved...
The rescue sequence at the end of the game, followed by the arrival in the Oubliette which provides the players with their first good look at the marvels of the pre-Collapse civilization
Doubling as a heartwarming moment, Tita gets one of these in SC when she stands in Loewe's way as he's about to kill Agate. The fact that she's facing the most dangerous person in the trilogy and an enormous dragon doesn't faze her and she tells Loewe in no uncertain terms that she will not move no matter what.
The return of Aureole in SC is pretty awesome, even if it is immediately followed by one of the biggest Mass "Oh, Crap!" moments in the series.
The one-on-one battle between Joshua and Loewe at the end of the game.
This really needs to be elaborated. First off, Loewe surmises that Joshua could probably win if he went all out because Loewe isn't as strong thanks to the previous boss fight but then tells Joshua to not count on it. Joshua does acknowledge this and goes for it anyway, displaying their prowess with one another. Loewe then manages to catch on and asks why Joshua isn't going faster when he knows his little brother can go for more when Joshua asks Loewe why he's still working for Ouroboros despite all of the things that have happened. Loewe starts his ranting when Joshua ultimately believes that Loewe is just living in a deluded world, especially when Joshua brings up Karin sacrificing her life for Joshua's sake. This did not sit well with Loewe who points out that he needs to test out if humans are worthy of Karin's sacrifice while Joshua fires back that his entire existence and life is all the answer Loewe needs. Not giving him any opportunities, Joshua proceeds to disarm Loewe with Loewe satisfied with Joshua's answer to his questions in life after Hamel.
In a way, Kevin and his Let's Get Dangerous! moment with Weissmann and the pillar of salt. The laidback flirty priest calling the Big Bad a heathen and then blasting him in the chest is one of those cool bits that forces you to completely reassess a character. Even with one story arc satisfyingly wrapped up, it really makes one want to beg XSEED for the next installment.
Operation "Clean Sweep." Arguably, THE most memorable Moment of Awesome in both chapters. While in most stories good guys(sans heroes) are out of the picture and / or incompetent this is definitely not one of those. And while baddies are all smug around women and children(most protagonists included here...) with Intelligence Division showing up in full force, bad guys lose no time running away.
The Big Damn Heroes moment at the top of Axis Pillar in SC is worthy in its own right but it's completely dwarfed by the corresponding scene in The 3rd: Kevin, Ries and Gilbert are trapped in Gehenna, surrounded by demons in sight of the gate to safety that they can't open. Just as things look grim, the gate opens and the remaining fourteen characters all show up and distract the demons long enough for everyone to escape. Yes, the characters effectively stormed Hell and lived to tell about it
The Arseille activation sequence at the end of The 3rd as the combined will of all the characters makes the ship not only move but exceed its normal limitations. The icing on the cake is that the following scene is Gilbert's personal Moment of Awesome
Gilbert pulling a You Shall Not Pass! by declaring that it's time for him to show the cast what he's really made of. Normally this would be something of a joke since the last three or four times he's said it he's been a pushover. He then directly manipulates Phantasma in order to summon his G-Apache and launches to hold off a Traumerei Dragion pursuing the Arseille. In the end it becomes a little funny when another two Dragion units show up to leave him hopelessly outmatched but he still manages to get all three pursuing him rather than the Arseille and that has to be worth something.
Being able to fight four of the Enforcers in a Wolfpack Boss battle was briefly teased at in SC, but in this game, you actually get to fight three of them at once. Better yet, the fourth one is a party member that can be brought to this battle.
When Kevin and Ries are sent to Gehenna, they manage to defeat Weissmann, Rostrum, and Astarte in a Wolfpack Boss battle, despite being outnumbered against three bosses who previously gave them trouble in Flunky Boss battles.
The Nightmare Arena has some truly amazing Dual Boss battles, like Kilika paired with Walter and Cassius paired with Loewe.