Summary:

Ash and his friends arrive at the beautiful land of Michina. Little did they expect to once again be found in a conflict between Dialga, Palkia, and Giratina. They are saved by a young woman called Sheena, who can communicate with a Pokémon's heart, and explains the whole conflict was because of Arceus being close to awakening. She also tells them that her ancestor Damos betrayed Arceus and stole the Jewel of Life, sending it into a rage and a slumber. Sheena plans to return the Jewel to Arceus.
After a small after-conflict, Arceus fully awakens and returns to Earth, using its signature move Judgment to destroy Michina. Arceus sees the Jewel is fake when Sheena tries to return it. Dialga, Palkia and Giratina return to try to stop Arceus, allowing Dialga to transport everyone but Kevin back in time to alter the past. They are nearly killed when Arceus attacks Damos and them, but Sheena contacts Dialga to send them further back in time. Arceus is apparently defeating the trio in the present day.
Ash, Brock, Dawn, and Sheena are several hours before Damos' betrayal. They are attacked by an army of soldiers and takes in everyone but Sheena, who manages to warn a man in a toga of what will happen and takes her for interrogation.
When Ash and his friends find Damos in their same space, they react very negatively at him, but Damos begins to explain what happened in the past. Arceus began to die after defending the Earth from annihilation from a meteor and losing its 16 plates; Damos helped find them and heal Arceus. In return, Arceus detached 5 of its plates to make The Jewel of Life to make Michina rich and fertile. Damos claims he has no intention of stealing the jewel. He also claims the man in the toga is called Marcus. Brock remembered that Marcus was present when Damos was supposed to give back the plate in the first time Dialga sent them to by mistake, and theorizes he may be the mastermind on this.
Hosting a dining for Sheena, Marcus is explained to by her Damos' true intent, and he agrees to help to stop him. He show an empty staff, which he secretly removed the jewel from, to Sheena, and goes to the temple with her. In the jail cell, a Notched-Ear Pichu befriended by Damos gives him the cell keys so they can escape.
At the temple, Arceus arrives and is told by Sheena that Damos will not be present. Marcus starts an attack, but Ash and his group arrives and Sheena comes to peace with her ancestor. Ash and Dawn confront Marcus with Pikachu and Piplup, but are overpowered by his Heatran and Bronzong. He then fights Marcus physically, but fails. Marcus drops the jewel and is recovered by Ash.
Arceus is weakening by Marcus's attack and Liquid metal starts getting poured on him. Damos and Sheena become able to communicate with Marcus's Pokémon which are being controlled by armor. Ash's Pikachu then destroys the armor, prompting Heatran and the other pokemon to rebel against Marcus. Arceus begins to die, causing a time paradox and Ash and his friends start to cease their existence. Ash's Pikachu fully vanishes, but before Ash fully disappears, he manages to give Arceus the Jewel back. The time paradox is canceled and everyone reappears and return to their proper time.
Expecting to find peace once again, they see Arceus has fully defeated Dialga, Palkia, and Giratina, and is preparing its final judgment. Ash cries out to it to remember that everything was fixed in the past. Arceus remembers and stops the attack, heals the dragon Pokémon, and restores Michina. The four dragon legends bid their final farewell to Ash and his friends and return to their respective dimensions.

http://en.wikipedia.org/wiki/Pok%C3%A9mon:_Arceus_and_the_Jewel_of_Life