CoroCoro Comics is running a manga adaptation of the film, Ruler of Illusions: Zoroark. Possible [probable?] movie spoilers ahead. I made a shorter, easier to read summary, by reading Volume 1, http://dogasu.bulbagarden.net/manga/movie_dp04/volume_one_01.html and the beginning of Volume 2: http://www.friendcodes.com/forums/blogs/yaminokame/11823-%5Bsummary-plot-spoilers%5D-part-2-1.html (and 2.2)
My summary is only based on everything so far - there'll eventually be 4 volumes total. Mouse over below to view spoiler'd text.


The antagonist, Kodai, interacted with the 'Ripple of Time' in the past [20 years ago], in a place called Crown City. The Ripple of Time is an energy created when Celebi travels from the future. Kodai used a small device on the Ripple of Time to gain it's energy, and thus the the power [inside of himself, not through a machine] to see visions of the future. An after effect of the Ripple of Time was killing the surrounding plant life in Crown City.
After gaining the power of precognition, Kodai then used it for his benefit in business, becoming a rich man.

In present time, Kodai's precognition ability is dwindling. Kodai saw a vision that Celebi returns to Crown City [for the first time in 20 years]. So, he seeks to once again gain power from the Ripple of Time. In a far away place, Kodai captures and contains a pair, Zoroa and Zoro'ark, in a cage, and travels by way of his huge boatplane to Crown City.
On the way to Crown City, Kodai uses a machine to create holograms of the 3 Beasts in front of Zoro'ark, and the Beasts attack Zoro'ark. Zoro'ark transforms into Raikou and attacks, believing they're real until the holograms go away and the training ends.
Then, Kodai takes away Zoroa, holding it hostage. Kodai tells Zoro'ark that if it wants it's baby Zoroa back, unharmed, Zoro'ark will have to do as Kodai says. Zoro'ark is pissed, but obviously must comply.

Zoroa ends up escaping from it's hostage, but Kodai keeps this information from Zoro'ark. When Ash meets Zoroa, we learn it has telepathy, and that Zoro'ark warned Zoroa to not use telepathy with humans.

Kodai, using Zoro'ark as a tool, unleashes Zoro'ark upon Crown City. Using it's ability to transform into the Beasts, Zoro'ark terrorizes the city and this forces the population flee. Kodai may now freely search to find the Ripple of Time. We also learn that the 3 beasts saved the city in the past (maybe 20 years ago?) so some people realised how strange it was that they would attack the city.

So that's the basic outline thus far. The 3 real beasts are controlled by some dude who's going to be a contender in the tournament of "Pokémon Baccer" - some sport that Crown City really grooves on, and a tournament for which is happening during the events of 'Ruler of Illusions: Zoro'ark'.