Delta Emerald Story

Why the Pokemon are Different
* ORAS Delta Episode Spoiler Warning*

During the Delta Episode, you are faced with a choice - whether to use the Link Cable to send the meteor to another dimension, or to obtain Rayquaza and destroy it. In game, you are required to obtain Rayquaza and thus use it to obliterate the meteor. Yet in an alternate dimension of ORAS, this does not happen and you use the Link Cable to send the meteor into yet another dimension, the dimension where Delta Emerald lies.

This is the meteor that ultimately creates Meteor Falls in this Delta Hoenn Region. Because this meteor is from another dimension, the radiation it gives off has caused Pokemon to obtain alternate attributes (in new Types, Abilities, and Stats) as mutations. Because it is a form of mutation, entirely new Pokemon are not created, and they are simply different forms of the Pokemon we all know and love.

Team Aqua & Team Magma
The goals of Team Aqua & Magma are slightly different in this dimension. Here, they want these mutated Pokemon to return to their normal states. Team Aqua plans to do this by awaking Kyogre so that it may summon heavy rain to wash away the radiation. Team Magma wants to do this by awaking Groundon so that the enhanced sunlight will burn away the radiation. Once these legendaries start to wreak havoc on Hoenn, they realize that it was silly of them to think that the radiation could just be washed/burnt away, and that it is okay for the mutated Pokemon to be different.

Castform
When you enter the Weather Institute, Team Aqua is trying to steal Castform because it is one of the few Pokemon seemingly uneffected by the radiation. They want to study it in their lab so they can find a cure for the mutations.

Spinda
Professor Cozmo is in Fallabor Town to study Spinda. Unlike Castform, Spinda is visually unchanged, but seems much more powerful.