The Way Better Ending to SEED
This starts off from where Providence arrives to attack Freedom and crew, only changes are that Fllay has the Strike-Rouge and was abducted by Le Creuset while inside the mobile suit so basically ZAFT had the Strike-Rouge until the battle of Jachin Due. Rau sent Fllay back with the "key" to ending the war just like the orginal series except this time instead of a shuttle she traveled via the Strike Rouge to the Dominion.
There everything went on like the original, except when Kira and co. were fighting the druggies Fllay betrayed them and went to help Kira and co. afterwards the 3 druggies managed to damage Fllay's suit pretty bad so Fllay went back to the Archangel. From there on all 3 druggies die the same way as they did in the series, the Rau vs. Mwu part is the same as Mwu comes back to the Archangel and REALLY dies from protecting the Archangel from the Dominion's positron cannon and Dominion gets destroyed the same way.
From there on just like the series Providence trashes Buster and Yzak destroys Raider, and Providence destroys the Meteor while Athrun decides to blow up GENESIS by self-destruction except this time Cagalli isn't there since she's on board the Kusanagi. Instead of killing Fllay which freaks out Kira, Rau made a big stab on the Eternal's bridge with his sword killing everyone on board, yes that means Lacus, Bartfeldt, DaCosta and crew. Since the Kusanagi was the closest ship to Yzak and Dearka, they were about to dock until they found out about Athrun's suicide attempt at destroying GENESIS, since Yzak's suit was more functional than Dearka's he decided to go alone to bring Athrun out while Dearka heads to the Kusanagi. Inside Yzak finds Athrun and while Athrun enables the codes to the self-destruct (NOTE: The Athrun and father thing already happened the only difference was Cagalli wasn't there to witness it.) mechanism on the Justice and Yzak decides to save Athrun from the explosion by taking him outside using the last bit power that the Duel has to get him out of GENESIS.
Outside, Kira and Rau have their final showdown where as Rau destroys Freedom's head and chest just like the series and and Freedom stabs him through the cockpit, but while the sword is inside Rau use's Providence's arms to hold on to Freedom so it can't escape and mentions that he'll take him down with him when GENESIS fires, right after that as a last act before GENESIS fires he activates a nuclear bomb that was put into the Strike-Rouge while it was on the Vaesalius, which means that the Archangel has exploded from the inside killing everyone on it. After, Rau does a laugh while Kira trying to find a way to escape but to no luck of finding it GENESIS fires destroying them both and Jachin Due explodes along with GENESIS. The only survivors were the members of the Kusanagi and Dearka, Yzak and Athrun, as the series ends from there.
--NOTES--
The ending is alot darker than the orginal ending of SEED but because of this kind of ending it gives the main character of Destiny, Shinn Asuka to keep his spotlight of main character now that Kira is dead.