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I don't care which theory was right either way but it just kinda sounds like the story of the game was poorly written, bad and confusing. I guess it just follows the pattern, I feel like these games stories have just been consistently shitty and underdeveloped yet attempt to be serious ever since USUM, where they plopped the ultra recon squad on top of the existing relatively competent SM story without any consideration whatsoever. They didn't realise the plot hole of immense magnitude they had created when lusamine did all the shit she did and her attempts to catch nebby when she had the ultra shit squad at her beck and call with a wormhole creating legendary the whole time. Just more typical modern gamefreak careless it seems to me.