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Deep down Aria already know Ulen project is the superior one nuking your own nation to kill one person confirmed that. The hatred Aura have for Kira is so strong it cost them the entire war all because he called her children murders. It was convenient they could placed the blame someone to attack a nation and try to place their DP plan on everyone.
Even though Kira and Lacus went into hiding at the end they will eventually be forced to come back out. That little retcon opened more doors for more people to have survive Mendel that Know about Kira and Lacus.
We still have Reverend Malchio who knew about Seed while others have no clue about it and he have connection to people that has not been shown.
If they make a third season I can easily see someone coming out revealing everything that link Cagalli past to Kira. People in the military know about Cagalli relationship with Athrun which would add more fuel to the fire if someone leaks it. Given what Foundation did to Moscow, Natural nations will blame Orb for everything leading to another war.
Everyone that link to Mendel is either dead or become the main villain for some reason. Lacus' mother and Reverend Malchio are the most two mysterious left that we know of.
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