I needed a place to not only document these combos as they come but explain why the combos actually work. On top of that I need to come up with some notation as well so I'll do that too.
And for full disclosure, all combos seen use Normal Play Mode. There's a Manual Play Mode which uses all the motions you're used to but since there's no punishment for using Normal Play controls you should just use those.
SR = Short Range Attack (Default Button B)
LR = Long Range Attack (Default Button A)
EW = Extra Weapon Attack (Default Button L)
TC = Thruster Cancel (Default Button R)
BAC = Berserk Activation Cancel (2+EW)
UA = Ultimate Attack (2+EW in Normal Play Mode/Varies in Manual Play Mode after a Berserk Activation)
All other notation is basic FG ones so no need to explain them.
Let's get into it!
jSR (4 Hits) → 6SR x 3 → 5EW → BAC → j8EW → 3SR → UA
The key to this and most of the stuff this game has to offer has to do with the majority of attacks happening on the first available frame in which they can happen. It's why that jSR does 4 hits instead of 2 or 3 in other cases. This is also true for the 6SR x 3 & the j.8EW. In the case of the 6SR x 3 is that in order to land that series is that each part of it has to come out as early as possible or the combo will end giving the opponent the chance to block or even counter in some instances. With the j8EW you have a couple of frames after the BAC to jump and do your EW attack and barely leave the ground so it connects. The rest of the combo will land itself. Just so you know, the 3SR isn't in this combo for show. You actually need it to land Chaos' UA because it functions as an anti-air outside of this instance. Enjoy.
j6LR → TC9SR → 5SR x2 → 6SR x 2 → 5SR (3 Hits) → BAC → 6SR x 2 → 5SR (3 Hits) → UA
j6LR → j3SR → 5SR x 3 → 6SR x 2 → 5SR (3 Hits) → BAC → TC9SR → 5SR x 2 → 6SR x 2 → 5SR (3 Hits) → UA
The thing that makes these combos so cool but a bit hard is getting used to are Thruster Cancels. Thruster Cancels follow the same rule as everything else in the game because any TC in question will come out on the first possible frame it can when activated. Landing the SR afterward is making sure your TC happens before doing your SR or you'll just be doing a 5SR on the ground instead. And treat TC's as you would a motion you Tiger Knee & a hyperhopping normal in KoF. They function on those same principals so keep that in mind.
6LR → SR x 2 → 6SR x 2 → 4SR (3 Hits) → 4EW (9 Hits) → BAC → 2SR x 2 → 6SR → UA
6LR → 5SR x 2 → 6SR x 2 → 4SR (3 Hits) → 4EW (9 Hits) → BAC → 5SR → 2SR x 2 → 6SR → UA
6LR → 5SR x 2 → 6SR x 2 → 4SR (3 Hits) → 6EW (8 Hits) → BAC → 5SR → 2SR x 2 → 6SR → UA
This combo has a whole bunch of variations but the 2 above are the hardest and most stylish to land and here's why. Starting off is that the 6LR doesn't lend itself too much to combos because the stun inflicted is so small so the only choice you have to even start a combo from it is a neutral SR attack but the upside is that the Aegis' SR's are so quick is that you can land 2 of them before branching further into the combo. The 6SR string & the 4SR are here for hit confirm purposes. The 4SR is a 3 hit command normal and on the 3rd hit you should cancel right into 4EW. The 4EW is the meat of the combo because this moves gives you so many hits to confirm your BAC to start the 2nd half of the combo. Know that the 4EW does 10 hits but for either combo we just need the 1st 9 because hit 10 causes a wall splat. Not only do we have our own later in the combo but for all intents and purposes is that you can do your UA off of this wall splat and most of the other moves in Aegis' arsenal as well if you BAC into it otherwise the recovery is way too long for you to do anything further afterwards. The same can be said for 6EW which does a wall splat on the 9th hit but follows the same combo convention.
The difference in the 3 combos is right here because either you can take your 9 hits and finish the combo, use the dash of the 10th hit of the 4EW to get in and land a 5SR for a tinge more damage and a hell of a lot of style points or do the 6EW for 8 hits which is the best damage option available with the added benefit of making the 5SR after the BAC a lot easier to connect on top that which makes it your best combo choice you have in this situation. The rest of the combo is pretty standard with 2SR x 2 → 6SR being the only way this combo lands without giving your opponent an opportunity to air tech it because the 6SR is our wall splat that allows the UA to combo. Weirdly enough is when the Aegis starts its Ultimate Attack is Athrun screams before unleashing that attack. Usually that sound effect doesn't play when his UA is comboed into from a wall splat because in most cases if you hear it then its a really high chance that the UA won't be comboed into naturally or even worse dropped all together.
Overall, you should learn the first variant and style with the 2nd one. The 2nd one doesn't do enough damage to even consider it in a match time situation and in most cases trying to go for it and missing at least gives you a chance at the first variant of the combo. However, if you can constantly style it then why the hell not go for it!
I'll be adding to this as I discover and make new videos that need dictation & explanation. Hopefully these combos spark your interest in playing & learning more about the intricacies of Gundam SEED Destiny.
-Triple Da G.O.D!