Mobile Suit Gundam SEED Destiny/WMG

There are two Cagallis.
Just like in Star Wars: The Phantom Menace, there's actually a Cagalli who is Izumi's daughter (and not Kira's sister) that the "original" Cagalli was surgically altered to resemble. After Gundam Seed, Athrun broke up with Kira's sister and started dating the identical appearing but totally different in personality Princess Cagalli. Princess Cagalli confused many outsiders who assumed the scrappy freedom fighter and the Princess were the same person.
 * Alternatively, the Cagalli of Destiny is a Skrull.
 * Or a Innovator mole. See below.

The Super Robot Wars version of Destiny is the canon one. The anime was propaganda created by Kira to make him look better.
Due to so many people saying "What the Hell, Hero?" over the course of the Second Bloody Valentine War, and the realization that he had been in the wrong while Shinn had been in the right, Kira commissioned an anime retelling of the war, subjecting Shinn to Flanderization and propelling Kira to godhood.
 * And now you know why Andy Waltfeld spends his time on TV Tropes instead of making coffee.
 * For this troper, the canon ending is split between this and Dynasty Warriors: Gundam 2, where Athrun runs around beating the crap out of anyone who even looks at him funny, Shin Asuka can make a case for his worldview without resorting to random screams, Kira himself thinks that what he's doing may not be right... and Lacus is painted as possibly-evil. This may also be a case of Author's Saving Throw.
 * for Dynasty Warriors: Gundam 2's Shin ending makes the most sense. The big fight happens, and Shin manages (by taking them off their high horses for a second to think about what they are doing) to best Kira and Athrun, while admitting that he is not purely in the right either. Everyone stops the fighting because they step up and admit that none of them is right. Bam, your logical happy ending.
 * Or we could just go with Master Asia beating the crap out of them.

Mu La Flaga did die at Jachin Due.
Neo Roanoke is another, more successful clone of Al Da Flaga, or of Mu himself, and his memories of being Mu are the result of some kind of previously-repressed psychic Newtype resonance between himself and Mu.
 * Alternately, the guy who died wasn't Mu. IIRC all we know about the extent of his memories is that he remembers being on the Archangel with his friends, not being in the final battle. Mu could have been replaced with a double sometime before the Battle of Jachin Due.
 * It's even easier than that. We already know that the Atlantic Federation has the technology to clone humans (see: the whole mess with Al Da Flaga) and to maniuplate memories (see: the Phantom Pain trio, particularly Stella). It's not to much of a stretch to believe that Neo is a clone of Mu with Mu's memories implanted (to make him badass as only Mu can be), and then with Neo's memories on top of that (in order to maintain his loyalty to the Atlantic Federation). If they figured out how to fix the short telomeres problem, or alternately figured out how to artificially age him to the "real" age of his genes, then no one would even ever know that he was actually a replacement.
 * Goddamit, Neo was a testbed for Full Frontal!

Cosmic Era Newtypes eventually play by After War Gundam X rules.
Next series, Kira will get his hands on a Destroy Freedom Gundam or somesuch with Satellite DRAGOONs, whose Satellite Cannons are tied to a limiter pendant carved from Evidence 01 by Andy and worn by Lacus. Eventually, however, he is brought down by Lowe Gear and his Astray Powered Red Frame Sturmangriff (Jess Rabble is driving the mecha horse). Afterwards, George Glenn's ghost calls forth an armada of space whales to destroy the PLANTs, deciding Coordinators really aren't worth all the Wangst.

The Space Whales evolved from humans.
If Turn A is canon & all Gundam stories take place in the same universe, they may be descendants of a previous generation of Newtypes. If not, they may be time travellers from a future where Coordinators have been altered so heavily they no longer resemble humans.
 * It's explicitly mentioned in Turn A that the space colonies fitted themselves with solar sails and headed into interstellar space. But the emergent Newtype phenomenon may involve the whales - the only non-human Newtype in Gundam was a dolphin in ''Gundam X, after all...

The plot is so screwed up because everyone in the series is suffering series wide Post Traumatic Stress Disorder.
When you think about, Gundam SEED was a non stop real life horror movie for the in universe people, both villain and good guy, and it didn't get any better at any point for ANYBODY. Even the ending didn't really lift the depressing feeling, and the "Break the World" incident followed by the failed nuclear assault on the PLANTS sure as hell didn't disabuse ANYONE that the horror had ended. Given that everyone is suffering neverending PTSD, it would explain Shinn's neverending Wangst, Durandal's idiotically idealistic "Destiny Plan", Rey's need to relive Creuset's f'ed up life, Logos' insistence on fighting a losing battle, and much of the repeated military idiocy on both sides.

In short, the whole universe of Gundam SEED Destiny is drenched in emo, and thus NO ONE was able to make a decent decision through its entire run.


 * This gets really funny/sad if you catch a little coincidence with the main three pilots: what other mecha anime is generally angsty, deals with PTSD, and contains a Shin, an Asuka, and a (in katakana) Rei? With names like that, the poor bastards were doomed from the start. Even better, Maaya Sakamoto went on to play another fiery female pilot with Zettai Ryouki for said show's Big Damn Movie.

Cagalli is, in fact, an Innovator who set about to sabotage SEED Destiny so it wouldn't be as hard of a an act to follow for 00
Cagalli's SEED powers are just careful misdirection and relabeling her Innovator skills. After discussing and planning everything out with Ribbons and comapany, she deliberately "picked" up the Idiot Ball as part of her Batman Gambit. From there, it was all a matter of Obfuscating Stupidity to throw everyone off while manipulating everyone off their character rails. Her piloting absence in Z stems from the fact people found out and naturally were furious. She was re-allowed to take part in K since 00 was wrapping up and the alleged Seasonal Rot had made her suffer enough.

Durandal and Shinn is the cynical Dumbledore/Harry mentor kind of relationship taken to its logical conclusion.
No seriously, hear me out. In a Dumbledore/Harry type of relationship the mentor is a protective figure, shielding them from other figures of authority, helping them out of trouble, excusing punishments or lessening them, secretly slipping them information, and looking the other way in regards to rules. They do this because they assure the hero that they are a good, heroic person, who only breaks the rules because he has a just reason and the mentor only trusts him to do this because he is special and trustworthy. Now, if you did this with a normal teenager, what would happen?

They'd let the power go their head and become a righteous little bastard, of course.

And what sort of person would let any kid, even a good one, get away with so much? Right, a mentor who is only using that kid for their own ends.

That's essentially why Shinn derailed at the end of the series. He's had an authoritive older figure that he greatly admires tell him that he is special and incredibly talented, rewards him with super powerful weapons, gets him out of trouble when he committed treason because they 'needed his strength', 'entrusted' with bringing peace and told that his motivations are just. Naturally, Shinn realizes he can get away with anything because he's always right, and everyone who disagrees must be wrong. He never reigns in his anger because he's rewarded for his results in battle. He's essentially kid who's been spoilt silly and then given keys to a super weapon.

Durandal, of course, isn't doing this because he thinks Shinn is so wonderful and perfect, but because he's very easy to manipulate. All he needs to do is butter him up, convert him to his side, and sic him on the enemy. He's basically got a dangerous attack dog that will never, ever question him. If Shinn ever died in battle and Dunrandal won, there's no question he'd move to the next young cadet.


 * That was Durandal's MO with prety much everyone, and for the most part it worked, Athrun is pretty much the only one who gets out of it, and only because he both had the experience of going trough a very similar thing with his father, and because the alleged deaths of his friends, coupled with being branded a traitor, pushed him well beyond the reach of Durandal's almost mind control powers. Shinn on the other had didn't have any such experience, obeying and blindly following Durandal had brought him nothing but rewards, he was a deeply troubled teen who rather than getting help for all his troubles had only been pushed further and further along the path of anger and self righteousnes, during the first ten episodes or so pretty much all we see him do is lash out at others and wangst in his room, all that changes as the series advances is that he is pretty much given acceptable targets to lash out again and convinced that his lashing out and attacking/killing anyone who disagress with him or Durandal is justified, because they are right. So yeah, poor kid never had a chance to stop his "character derailment".

Fllay and Lacus were actually the same person and Lacus is Seed Destiny is the Rau. And 'Jesus Yamato' is actually a clone of Kira made by him.
In the beginning there was the Multi-Verse, the original idea of SEED with Fllay as a pilot and a tragic ending where her and Kira truely loved one another and were killed in combat. When the multiverse combined Lacus and Fllay were different enough that they existed as seperate beings instead of combining like other characters, Fllay was afraid she would cease to exist if Lacus came around and when Rau killed her she simply reunited with Lacus. However when Kira killed Rau he used his Newtype powers to place a part of his Psyche into Lacus and slowly take her over.

A few things happen now, Lacus meets a young Meer and transfers the combined Lacus/Fllay persona into her, which is why she believed she was Lacus but still felt fake. Kira who was depressed from Fllays death retreated to an undisclosed location and studied cloning creating a clone of himself, a being who could serve justice and feel emotions but never get emotionally connected to feel the pain he felt. He dubbed the clone 'Jesus' Yamato and sent it into the world to replace him. Meer met Durendal and explained the situation who promised her that he would prevent Rau from carrying out whatever plan he has and helps raise Rey into an opposite of Rau and he takes Shinn as his personal choice for a Champion.

The destiny plan called for Shinn to be mentored by Rey who would then be tragiclly killed in battle causing Shinn to seek to protect the world from anything along side the help of his girlfriend Lunamaria. The problem was with JESUS Yamato now replacing Kira Meer couldn't contact him for the plan and uncontested Rau took over Lacus and pretended to be her.

The assaination attempts were staged poorly by Rau himself to throw suspicion onto Durendal who he felt was a possible threat to him, Durendal getting flustered when Rau took over the television broadcast was because he was a fake Lacus. In truth he DID have the real Lacus Clyne.

At some point Lacus and Fllay body hopped into Cagalli who needed to wait for a time when Rau was weak to put them back into there body and stomp Rau out. The problem was that Durendal had to alter the Destiny Plan to stop Rau from creating a giant war, using the tested and working method from mars he attempted to put the same system in place on Earth but left the option open for any company to refuse it, Scandinavia and Orb refused but Orb chose to react violently as Durendal grew more frustrated with Rau. Hence the final battle of the series and Jesus being a near invincible god. Now a lot of this needs proper placement since I forget events but the end result is that Lacus was Rau, Kira was a clone and Durendal was a tragic good guy.
 * gee, thanks for turning Gundam SEED Destiny into TsubasaChronicle. Thanks a fucking million.

Durandal has mind control powers
Explains Shinn's actions in the last quarter of the series perfectly, beginning from the scene when he was chasing Athrun. He seems confused and torn about his motivations and actions, stuck between what his best friend and his respected commander is saying. Then, he thinks of what Durandal said, and BAM, mind control kicks in, and all the doubts float away to be replaced with a firm belief that anything that Durandal says= truth, therefore if Durandal says that his plan will end war, then anyone who is against Durandal is against ending war.
 * On the flip side, this explains why Kira and co were unaffected by the mind control, as Kira's Ultimated Coordinator trait serves as an amplifier for Lacus' own mind control capabilities in the same way Rey amplifies Durandal, and thus Lacus was able to maintain a strong control over the rest of the crew and prevent the influence of Durandal's words from spreading within her own territory. Due to the bond shared with Lacus, Kira was also able to inherit the ability to at the very least influence people's minds, and while Athrun's mental defense was able to hold off Durandal's control, the resulting exhaustion left him helpless against Kira's weaker influence, thus leading to him switching sides. Also, in the dual between Kira and Rey, while equal in piloting capabilities, Rey lacked the ability to counter against Kira's inherited psychic abilities. Despite sporting a strong mental defense thanks to Durandal's prolonged influence, Rey eventually cracked under the continuous psychic bombardment of Kira, who was trained under the guidance of Lacus in the arts. Basically, Gundam SEED Destiny was one massive cover-up on a psychic war that occurred between two exceptional minds, Durandal and Lacus. People of unprotected minds have been known to go insane upon hearing the recordings of exchanges made over the communication devices of mobile suits.
 * It scares me how much that makes sense...

Lunamaria and Shinn's relationship
Luna always admired and loved Athrun because of his status, but also admired Shinn for his piloting ability. When she found out Athrun had betrayed them, she was at a loss. How could the man she admired so much have betrayed them? To make matters worse, her sister had also left with him. Their deaths left a huge hole in her heart. Then, she sees Shinn, the man who killed them, apologising to her. She collapses crying onto him, and he holds her, comforting her. This man, who is a great ace like Athrun, is comforting her in ways Athrun never did, even though he is the one that killed her preciosu sister. The next day, she is given his old mobile suit. They talk before going into battle, and Luna comes to the conclusion that Athrun betrayed them, 'tricked' them for all this time. She writes off Meyrins betrayal as Athrun 'tricking' her, giving Luna another reason to hate him. However, this love she has for Athrun won't go away. So she goes to the next best thing, Shinn Asuka, ace pilot, who comforts her and says he'll protect her. Luna convinces herself that she really loves Shinn, and hates Athrun. This allows her to patch up the wounds created by the loss of her crush and her sister.

Shinn had already lost two girls in his life. He's already failed to protect two people he loved. And now, a person he truly trusts had betrayed them, running away. Shinn is torn. He can't match the Athrun that he trusts and admires with the Athrun that just told him the path he is following is wrong. Shinn remembers the people he lost, and goes into a rage. How dare this stuck-up person say that he is wrong? He was trying to stop any of these losses happening again. He followed this path for that reason. Therefore Athrun must be wrong. He must want these tragedies to keep happening. So Shinn goes into a rage, and destroys the suit with Athrun and Meyrin in. Then, he goes back to the ship, and sees Luna. The sister of the girl he killed. He says 'sorry'. What else can he say? He was right, Athrun was wrong, therefore anyone with Athrun must be wrong. Then Luna starts the cry. She clings to him and sobs into his clothes. Suddenly, Shinn remembers. Stellar used to cry like this. Stellar would stop crying when he held her. So Shinn holds onto Luna, to block out the memories of Stellar, so he doesn't have to see the similarities between her and Luna. The next day, Luna seems scared about going into battle. Stellar used to be scared of going into battles. So Shinn tells her that he will protect her, because that's what he'd tell Stellar. Then, Luna hugs him again. Shinn understands. This girl needs his support, like Stellar did. He won't fail this time. And he remembers Stellar's last words, 'I love you'. That must be why he couldn't protect Stellar, because he didn't love her enough. So Shinn kisses Luna. He decides he will love this girl, love and protect her, and therefore stop the pain of the past, and so he will never lose a girl he cares about again.

(This doesn't explain how Shinn/Luna is true love, but it makes sort of sense for how it began. I suppose it could grow from here, like Kira/Flay, or something.)


 * Or, you know, you are entirely right and it is NOT true love, at all, more like Shinn taking advantage of Luna's frail emotional state, which he caused to begin with, and her need for support, on top of being on the rebound. Likewise, Luna was in a bad place so she latched onto the first person to offer her comfort, so it's just a screwed relationship of codependence, which fits Shinn down to a t, Luna not so much, but as mentioned early, she was emotionally fragile at that moment.
 * Or Shinn and Luna were both feeling emotionally vulnerable and needed something to cling onto. Relationships start fast in wars, largely due to the stress of the moment. Look at the number of infantrymen who came back from WWI and WWII married to nurses or locals who they'd often known for at most a few days or weeks. Now contrast that with Shinn and Luna, who have been friends for years and who, in a moment of emotional need turned to one another. It doesn't hurt that Shinn apologised to Luna for shooting down Meyrin.It's one of the few times in the show that Shinn's apologised for anything and Luna knows it, which helps explain why she isn't furious at him. And on top of that, they don't actually kiss (thus signifying that they are in a relationship) until a couple of episodes later. Shinn and Luna may be annoying in terms of plot, but it makes perfect sense in the context of the war.

Luna never loved Athrun at all and was merely keeping tabs on him
Luna was the one who observed Athrun during his meeting with Kira, seeing if he was going to be truly loyal to ZAFT. Any and all attempts to romance him were merely under orders and make sure that Athrun Zala, one of the great ZAFT's heroes-turned-traitors, stayed with them this time. Her interest in Shinn, however, was genuine, and her opening up to him after he apparently killed Athrun stemmed not only from grief of Meyrin's death but also the first chance to ever show him that she did care for him.

Phantom Pain was a testbed for Newtype pilots
The Federation realised how awesome Newtypes guys with enhanced spatial awareness were from their experience with Mobius pilots, so they created Phantom Pain to find people with any trace of the ability and try to unlock their full potential. This explains why they went to the effort to revive and brainwash Mu, and why the Destroy Gundam (intended for Phantom Pain use) has DRAGOON-like weaponry. Stella scored the highest on their tests (this is why Neo insists on using her as the Destroy's pilot), but ultimately the project was a failure.

Gilbert Durandal is a Time Lord
He regenerated into Ingram Prisken. They have the same hair.

Logos Does Not Exist
Or at least not in the form that Durandal claims it does. Think about it: Durandal claims that Logos is an Ancient Conspiracy that convinces people who would normally be all about peace and love to go to war with one another and commit rampant slaughter. He claims that Blue Cosmos is just a front for them, and that Djibril is really interested in making money, not killing every Coordinator. He then proceeds to produce a list of politicians (all of whom just happen to be his enemies) who are Logos members.

Seriously, stop and read that over a couple of times. Without Durandal's oratorical ability behind it, that sounds ridiculous doesn't it? Wait, it gets worse. Even if you accept what Durandal says at face value, there are two more huge stumbling blocks to the "Logos as Ancient Conspiracy theory".

1: There are apparently no members inside ZAFT. If you were running an organisation dedicated to convincing people to go to war with one another so that you could sell weapons to both sides, wouldn't it make sense to have people in both camps? After all, it's not like you're hindered by ideology or convictions or anything like that, it's all about the money, right? Yet Logos not only has no members in ZAFT, it apparently has no members in the Earth Forces countries that support Durandal. We aren't told that they've been arrested or anything like that, they just don't seem to be there. Isn't that suspicious?

2: If Blue Cosmos is just a front, than that means that Djibril and Azrael were both faking their hatred of Coordinators. Full stop. That simply isn't possible. Both men were absolutely consumed with hatred for Coordinators. Azrael died leading a nuclear assault on ZAFT, and Djibril is ecstatic when he fires Requiem at Durandal and the colonies. And they aren't stooges or dupes or anything like that, Durandal says flat out that Djibril is the leader of Logos. And another point, connected to this one: there is no profit in the apocalypse. If Logos is out to make money through war it should be setting off dozens of little ones, not trying to support an all out genocide that will result in the deaths of half their clientele. It's not only evil, it's bad business.

When I first watched this show, I assumed that Durandal had invented Logos, and was claiming that all of his political enemies belonged to it in order to get them arrested or killed without making himself hated. Rewatching it, I realised that Djibril does mention the name during one of his early appearances. He never however, says what Logos does. My theory therefore, goes like this: Logos is a global network of hate groups, including Blue Cosmos, and a variety of other anti-Coordinator and racist organisations in other countries. Durandal, found out about this network, and decided to use them to justify his war, but very cleverly, fudged their real purpose. After all, saying that he's after anti-Coordinator groups wouldn't necessarily get him a lot of Natural support. Saying he's after a group that deliberately engineers wars in order to profit from them, on the other hand, will get him the support of every gullible person who isn't a total psychopath. Moreover, it allows him to add people to his list of "Logos" members who aren't affiliated with Blue Cosmos or any of its associates.

Why is this important? Because it let's him start a witch-hunt against any Earth politician--Blue Cosmos member or not--who might be able to rally people against the Destiny Plan. All Durandal has to say is "he's a member of Logos" and the poor sap's career is over. He/she can't even deny it by saying they aren't a Blue Cosmos member or that they have a pro-Coordinator record, because after all, that's not what Durandal's accusing them of. He's accusing them of being rich, and powerful, and in a position to influence the outcome of the war. Durandal can keep adding people to his list (and does: remember when he and Rey told Shinn that both Athrun and Cagalli's Orb had sold out to Logos?) and no one will ever question him, since he's the only one who supposedly has the list of Logos' members. At any other point in time this plan would be ludicrous, but in a climate of fear and uncertainity like the one in Destiny, it can (and almost does) succeed brilliantly. The people of earth are so desperate for peace and an end to the bloodshed that they'll accept everything Durandal says as proof and follow the Chairman into his Brave New World, convinced that they've rid themselves of the evil-doers in their midst when in reality, all they've done is kill the only people who might have kept them independent.

In conclusion, Logos is a sham, a fraud, a fantasy concocted by Durandal in order to give the people of Earth something to turn their hatred against. It allows the Chairman to elminate all his rivals swiftly and efficently, all while continuing to appear to be an accepting Messiah figure.
 * A possible variation of this: LOGOS is actually a loosely-affiliated network of rich and powerful naturals who just don't give a damn about anyone else. Much like the colonial powers of preceding centuries, the members of this group are a high-class clique who use the colonies to make money - no matter the moral consequences. Hence, they were anti-coordinator. But, they're anti-coordinator in the same way that former imperial governments were racist (i.e. not the same way as, say, the Nazis were racist). They don't want to wipe anyone out - they just want to oppress and exploit them for every penny. Azrael and Djibril were the only ones who really wanted them all killed off, largely due to their own messed up child-hoods. This group has existed since long before the space age, as mentioned previously, but existed in different incarnations, not as a single monolithic conspiracy. It didn't get a name like LOGOS until later - that is, unless Durandal made that up as a part of his embellishment. Basically, Durandal took this "gentlemen's agreement" and Flanderized it into an ancient conspiracy that sought only to make money through wars. While this is not an outright lie, every falsehood contains some cleverly disguised truth. The known members couldn't try to set the record straight due to their true nature not being all that great, either. That's why they had no members in the PLANTS or ZAFT-aligned nations, they either didn't have any members who fit the criteria (a natural with no love for the coordinators and wanted to get rich), or the members sensibly fled before the crap hit the fan.
 * Although I stand by the rest of my variation, strike the last bit of my above addition: According to the Gundam Wiki and hints from the creators, ZAFT may have allegedly had a member of LOGOS in their midst the entire time: Gilbert fucking Durandal. As well, he was the one who manipulated Canard Pars into wanting to kill Kira (in the manga spinoff), and he may have had a part in the Ultimate Coordinator Project. That Magnificent Bastard...

Lacus is another Ultimate Coordinator
For one thing, it's obvious that she possesses a SEED factor like Kira. For example, when she is contemplating the nature of war in episode 49 of Gundam SEED, you can see that her eyes have dialated, indicating that she has entered 'SEED mode'. However, the real smoking gun is when you realize that she seems to have the same ESP factor unique to those connected with the Ultimate Coordinator project. When Rau attacked the Eternal during the final battle, Lacus commented on a 'strange feeling', much like Mu and Kira had commented on earlier. Plus, in Destiny, she seems to be able to sense Kira too, and vice versa, such as when the Eternal is under attack by ZAFT and during the final battle when Kira returns from wreaking Rey's machine. Since it's unlikely that she's a clone like Rau and Rey, the only other option is that she is, like Kira, an Ulimate Coordinator, or at least an imperfect one like Canard.
 * Also, she's the Author Avatar of Morosawa.

There are two kinds of Coordinators
On the one hand you have the combatants, graced with enhanced reaction times, resistance to G forces, ect. Like Shinn, Athrun and the majority in existance. On the other you have the leaders, like Lacus and Durandal, graced with manipulative ability and frightning charisma. The two kinds exist to do diffrent jobs, hence diffrent genetic predispositions. the Destany Plan is essentally built off that concept. So what is Kira? 'The Ultimate Coordinator' Ultimate as in Final. A Coordinator with both combat and leadership potental, explaining how he can both win mobile suit battles and sway people. Worse, the combination of reaction time and ability to read bodylanguage (which can to a point be translated to mobile suits) has a synergistic effect. He seems to react to people impossibly fast because he is reading their cues faster, and then reacting faster on top of that.

Rau le Creuset engineered the entire Bloody Valentine War
There were a couple coincidences that went into making the war play out the way it did. None of them so egregious that they're obviously suspicious, but they do form a noticeable pattern, and as a high-ranking ZAFT commander in contact with the other side, Rau would have been able to make them happen. He seems to have a particular style. He masks his true objective behind a larger tragedy.
 * First, the bombing of the UN meeting on the moon. All of the delegates were killed except for Seigel Clyne, who was delayed by a shuttle malfunction. This provided the excuse the sponsor nations needed to declare war. Rau could have sabotaged the shuttle, or arranged for it, as well as directing the terrorists who carried out the attack.
 * Second, the nuclear attack on Junius 7. It was not the only agricultural PLANT colony, but it just happened to be the one where Lenore Zala, wife of PLANT Defense Chairman Patrick Zala, happened to be on that day. This led to Zala eventually having a complete breakdown and trying to glass the entire Earth. Rau could have found out Lenore Zala's travel plans and directed Muruta Azrael to have his men target that PLANT specifically.
 * Third, the deployment of the neutron jammers in Earth's crust. Prior to this, ZAFT always showed immense patience and restraint when dealing with the Earth. Even when the Earth Forces were revealed to be behind the attempted assassination of the PLANT Supreme Council (which succeeded in killing only one chairperson) a few months before the actual beginning of the war, they still did not react aggressively. When the war did start, they only deployed the jammers on their cruisers. Deploying them on Earth caused a massive energy crisis resulting in millions of deaths, but it also allowed ZAFT to start making headway against the massive numerical superiority of their foes. Rau could have suggested the strategy intending to sway public opinion on Earth against the coordinators.
 * Fourth, the use of the Cyclops superweapon on the Grimaldi front. This ended a theater of the war, as the supply base that was its objective was destroyed, and also resulted in massive casualties on both sides, including every single one of the Atlantic Federation's Mobius Zero corps, except for Mu la Flaga, who Rau would later complain was always getting in his way. Rau could have suggested the tactic to Azrael, hoping to both escalate the war and eliminate the obstacle Mu and his comrades represented, as they were essentially if not literally newtypes and stronger than almost any coordinator.
 * Fifth, the destruction of the Silverwind. The Silverwind was a civilian passenger ship carrying Lacus Clyne on an inspection of Junius 7, lost with all hands and passengers except for her, as she was put into an escape pod beforehand. If the ship were chartered early enough, Rau could have gotten wind of its course and asked Azrael to ensure a ship with a strongly anti-coordinator crew just happened to be in the area. If Lacus were killed, it might have had the same effect on Siegel Clyne as Lenore Zala's death had on her husband.
 * Also, there are the events he is known to be responsible for. The destruction of Heliopolis, reportedly an accident partially caused by the use of heavy weaponry inside the colony by ZAFT forces, reduced Orb's influence in space and threw the troublesome neutral nation into political turmoil. The Cyclops system used at JOSH-A, which eliminated much of the more moderate Eurasian Federation's military power and reduced their influence. And, of course, the renewed deployment of nukes against the PLAN Ts and GENESIS against the Earth by Rau's puppets Muruta Azrael and Patrick Zala, once the war escalated to the point where Rau knew they would be used for genocide.
 * Alternately, Le Creuset was just behind the nuclear attack. Tensions were already at a boil and all Rau had to do to make it boil over was give Azrael a way through ZAFT's defences. Azrael's foreign policy can best be summed up as "when you have enemies, you shoot them," something that Le Creuset would have figured out after about ten seconds interacting with the man. The rest of the war was easy to improvise: latch on to the ZAFT commander with the biggest grudge against the Naturals (if it hadn't been Patrick he could have easily selected somebody else; with Rau's brains behind them they would have been Commander-in-Chief soon enough), and ensure his rise to power while still feeding Azrael information. With both sides led by hardliners he didn't need to engineer anything else beyond the eventual use of the superweapons; there certainly wasn't going to be a compromise as long as Azrael was alive. Same basic idea, just more Manipulative Bastard and less Chessmaster.

Lacus Dust = Predecessor to GN Particles?

 * Several websites (notably, the Animesuki forums) make a reference to Lacus Dust, which explains why Kira became a John Cena-esque God Mode Sue in the later episodes of both SEED and SEED Destiny. It can also explain why both Andrew and Mu (and if we go outside of CE, Zechs) came back from the dead. I don't know when the Lacus Dust jokes began, but I think that Sunrise might have adopted the Lacus Dust concept and adapted it as GN Particles for 00.
 * In other words, a wizard Lacus Dust did it.

Neo Died When He Intercepted the Tannhauser

 * Prior to his attempted sacrifice, Neo may be acting more like La Flaga, but he still lacks the memory and emotional depth of his predecessor. He may like Ramius and Kira, but that's largely based on the fact that they seem to know about his past, something he has to be curious about. It's only after he flies into the Tannhauser's blast that he regains his memory and acts like Mu again. I'd contend that what we've actually witnessed is not so much the return of Mu's memory, as it was the death of the "Neo" persona. Having learned to care about Ramius and the others aboard the Archangel, Neo, previously a cold-blooded Manipulative Bastard makes a Heroic Sacrifice, and in the shock of the positron blast, dies, mimicking La Flaga's Character Development in SEED and allowing the latter to come back to life. He didn't lose Neo's memories of course, but the actual personality (best defined by manipulation and self-loathing)? It died.

Durandal might have lost the war, but he still won the argument when it comes to the Destiny Plan.

 * I was lurking at the Easymodo archives, and one of the posters suggested that although Durandal lost the war, he was more or less proven right about the Destiny Plan theory. He very much forced Kira and Lacus to become what they didn't want to be; in Kira's case, becoming a soldier, and in Lacus's case, becoming the new ZAFT chairwoman. In other words, they were destined for their roles.
 * So by having his entire plan destroyed--meaning no one else will have to fullfill the role he believes they should--but getting two people to do something they didn't want to he won the argument? That makes sense. Besides how do we even know that "soldier" and "politician" are what Kira and Lacus are best suited for? They're good at it, but that doesn't necessarily equate to "perfectly suited for it genetically". And oh yeah--they're doing it because they want to, not because their genetics told them to.