The girls use their special powers, which they recieved when merged with the animal DNA, to fight off kirema animas, which are animals taken over by the aliens. In order to stop the aliens for good the girls are trying to collect what are called Mew Aquas.
And as if life wasn't hard enough, Ichigo is trying to maintain a relationship with Masaya, who is her boyfriend while trying to keep being a Mew Mew a secret.
Stressful neh?
on a personal note, I loved the manga and though I haven't seen much of the anime, what I have seen looks very good.
-shadow