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However she was in control of Edea for over the course of the first two disk, the speech she gave when President Deling introduced her, that was Ultimecia speaking, the clothes that Edea wore when under Ultimecia's control are a stark contrast to the simple black dress she is seen wearing in the flashbacks and at the end of the game.
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She does seem to view SeeD as a persistent nuisance in her little speech, but the abovementioned attempts prove that SeeD is a serious threat to her at the very least. This is further compounded by the fact that she actually points towards this in the opening monologue of the final battle: that SeeD were "swarming like locusts across generations." On its own, this little statement implies that SeeD hasn't quit pestering her for quite some time ("across generations") and she never truly got over that particular obstacle.Looking at this evidence, there is an alternate conclusion as to the "bad" future: SeeD was winning the war and Ultimecia's use of the Junction Machine Ellone was a Skynet-esque desperation tactic to stave off defeat - in which case, the happy ending is reinforced, not ruined. Heck, the first thing she does when she takes over Galbadia in the past is to attempt to destroy Garden and thus wipe out the SeeDs before they even really exist. And Ultimecia is desperately trying to engage Time Compression. Hell, some parts of the castle appear to have been hit by artillery fire.
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Ultimecia's castle is devoid of soldiers or real security measures. However, look closer the dead SeeDs are within line of sight of Ultimecia's castle. Some people concluded that in Final Fantasy VIII, there's a Bad Future where Ultimecia has wiped out SeeD and rules the world, and this is guaranteed by a Stable Time Loop.This can be seen as a running joke in the game, or it could be alluding to how terribly the GF induced memory loss is affecting Squall. He forgets about "familiar looking guy" in Fisherman's Horizon and he even forgets Nida, who became a SeeD with him. Throughout the game, Squall sometimes forgets people he meets quickly.As a Fridge subpage, all spoilers are unmarked as per policy.