The Milkshake Swamp is home to grass and poison type Pokémon. Beware of the Posion Ivy, it may be a shortcut through the forest, but it will poison your Pokémon. To the northeast of the forest are ruins.
Spoiler warning: this article may contain major plot or ending details.
As you reach the ruins, you'll see that Team Fusion is up to no good investigating the ruins. By the time you get there it's already too late. Blake will try to protect the Inventor and you fight off the Grunt. By doing this you receive the Pokécomm to understand Pokémon's thoughts! Unfortunately, you once again slip through the universe and land in the Green Swamp.
In the Green Swamp, the man from before introduces himself as Luke and asks you to hunt down a Mudkip. Find the Mudkip and catch it (there's only one in the game!). After that you return to Milkshake Swamp.
Finish out the last few trainers and proceed to Oceanview Park.