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>Mossdeep develops its space program, discovers a new planet capable of harboring life, but devoid of it
>the remnants of team plasma, galactic and aqua/magma form a new organization called Team Cosmic, under a new leader
>goal is to create a new, better planet for Pokemon and separate them from humans
>take over space program
>obtain Deoxys samples and use them to clone the weather trio
>travel to new planet, use legendary clones to terraform it to their liking
>using a device based on the events at Spear Pillar, powered by residual energies from the creation trio, open a portal between the worlds
>protag travels through it to stop them, fights the team, fights the legendaries, etc
>amidst all the fighting, the real Deoxys shows up, prompting everyone back through the portal and off the planet, and dissipates itself into it, sewing the seeds of life so that, rather than imitating other life forms, it can become its own naturally developing organism
>a new pokemon planet is born