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Team Magma first appear in the 2nd Advanced Episode if I remember right and a Team Aqua member first appears in "Stairway to Devon" As far as motives go, in the games Magma want to make the whole world covered with land if I remember right and Aqua wants a world covered with water....
....yes their motives are strange ones.
the reason their motives r so strange is that thats the ritual to awakening kyogre and groudon and magma and aqua r in a race to summond them 1st.
if aqua summonds kyogre first the drizzle created by it will flood the world with water and magma wont be able to awaken groudon bcuz it cant survive with so much water.
if magma summonds groudon first the drought created by it will overheat the world with land everywhere and aqua wont be able to awaken kyogre bcuz it cant survive with so much heat.
so its all just a compitition....and i believe team rocket wants the commanding power of mew and mewtwo.
We really don't know what the motives of Team Aqua or Team Magma in the show are, not yet. Based on the games, Aqua wants a world of water so Pok?mon can thrive and Team Magma wants a world of land so people can thrive. You choose whose more 'evil'!
If their motives were the same, then how in the world will they introduce Groudon and Kyogre???
Niether of them are evil(but Team Aqua is obviously better though). Team Magma thinks that a world made of only land is better because Humans and Pok?mon alike can thrive on land. Team Aqua thinks that a world covered in water is better because there are so many water Pok?mon and they think that humans and non-water Pok?mon could adapt or just live upon floating stuff. Team Magma wants Groudon because it has the power of ground/fire which can dispose of all the water. Team Aqua want Kyogre because it has the power of water which can cover the land with water.
Team Magma's intention was kinda revealed during the sixth movie. Team Magma is planning to revive the Pok?mon Groundon, by any means neccesary. Faillure is not an option and will result in being banned from the team by the high leaders. This happend to a man called "Butler" (I don't know why the writers would give him such a name). He build a machine to bring Groundon back to live using a small piece of Groudon's skin. Due to power shortage the experiment failed and he was humiliated and banned from Team Magma.
Also Team Magma seems to have many connections to obtain information and even rare artifacts. A Team Magma member said in the 2nd Advanced episode: "As you can see, we have many friends at high places". They worship Groudon like it is a supreme being or something (or at least in the games). But it is still unclear why Team Magma want to revive Groudon in the anime.