Plot In 1936, archaeologist Indiana Jones (or Indy), and Sora brave an ancient booby trapped temple in Peru and retrieves a golden idol. Upon fleeing the temple, Indy and Sora are confronted by rival archaeologist René Belloq and the indigenous Hovitos. Surrounded and outnumbered, Indy, Sora and friends are forced to surrender the idol to Belloq. Indy, Sora and friends then escape aboard a waiting Waco seaplane after being pursued.
Shortly after returning to Marshall College, where he teaches archaeology, Indy is interviewed by two Army intelligence agents. They inform them that the Nazis, in their quest for occult power, are searching for his old mentor, Abner Ravenwood, who is the leading expert on the ancient Egyptian city of Tanis and possesses the headpiece of the Staff of Ra. Indy deduces that the Nazis are searching for Tanis because it is believed to be the location of the Ark of the Covenant; the Nazis believe that if they acquire it, their armies will become invincible. The Staff of Ra, meanwhile, is the key to finding the Well of Souls, a secret chamber in which the Ark is buried.
The agents subsequently authorize Indy, Sora and friends to recover the Ark before the Nazis. With help from Ash Ketchum, Misty, Brock, Pikachu, Togepi, Sly Cooper, Bentley, Murray, Gordon Quid, Waffle, Mr. Blik, Jean-Bob, Speed, Puffin, CatDog, Timon, Pumbaa and Samurai Jack. The group travels to Nepal, only to find that Ravenwood has died and that the headpiece is in the possession of his daughter, Marion, who is also Indy's embittered former lover. Indy offers to buy the headpiece for $3000, plus $2000 more when they return to the United States. CatDog also offers a diamond. Marion's tavern is suddenly raided by a group of thugs commanded by Nazi agent Toht. The tavern is burned down in the ensuing fight, during which Toht burns his hand on the searing hot headpiece as he tries to grab it. Indy, Marion, Sora, Ash and their friends escape with the headpiece, with Marion declaring she will accompany them in the search for the Ark so he can repay his debt. On the way, Circuit hands the team the bible so they can learn more about Ark, but only Bentley read the most out of it.
They travel to Cairo where they learn from Indy's friend Sallah, a skilled excavator, that Belloq and the Nazis, led by Colonel Dietrich, are currently digging for the Well of Souls with a replica of the headpiece modeled after the scar on Toht's hand. In a bazaar, Nazi operatives attempt to kidnap Marion and as Indy, Sora, Ash and their friends chase after them it appears that she "dies" in an explosion. While deciphering the markings on the headpiece, Indy, Sora, Ash and Sallah realize that the Nazis have miscalculated the location of the Well of Souls. Using this to their advantage, they infiltrate the Nazi dig and use the Staff of Ra to determine the location correctly and uncover the Well of Souls, which is filled with snakes. Indy and Sora fend off the snakes despite his ophidiophobia, with the team behind and acquire the Ark. Inside the well, the team finds a picture of a weapon that looks just like a Keyblade. meaning that is the only way to seal the Ark! Then some of the team gets into an conversation with Sora because they think the Keyblade is the only way to seal the Ark for eternity. But then Belloq, Dietrich, and the Nazis arrive to take the Ark. They toss Marion into the well with Indy, Sora, Ash and their friends and seal them in, but they manage to escape. After a fistfight with a Nazi mechanic, blowing up a flying wing on the airstrip, and chasing down a convoy of trucks, Indy, Sora and the others take back the Ark before it can be shipped to Berlin.
Indy and Marion leave Cairo to escort the Ark to England on board a tramp steamer. The next morning, their boat is boarded by Belloq, Dietrich, and the Nazis, who once again steal the Ark and kidnap Marion. But before they take Sora, Ash and their friends uses the Cooper Van to go underwater. Indy stows away on their U-boat while the team builds a raft out of crates and barrels and then follows them to an isolated island in the Aegean Sea where Belloq plans to test the power of the Ark before presenting it to Hitler. Indy reveals himself and threatens to destroy the Ark with a bazooka, but Belloq calls his bluff, knowing Indy cannot bear to destroy such an important historical artifact.
Indy surrenders and is tied to a post with Marion while the team's put into a crystal box as Belloq performs a ceremonial opening of the Ark, which appears to contain nothing but sand. Suddenly, spirits resembling Old Testament Seraphim emerge from the Ark. Aware of the supernatural danger of looking at the opened Ark, Indy warns Marion to close her eyes. Meanwhile, the apparitions suddenly morph into "angels of death", and all of the Nazi soldiers, along with Belloq and Toht, are gruesomely killed. After the Ark's power's released, Sora and her friends are left speechless by God's power and then Sora seals the Ark's Keyhole to locked it for all eternity.
In Washington, D.C., the Army intelligence agents tell a suspicious Indy and Brody that the Ark "is someplace safe" to be studied by "top men". The Ark is permanently stored in a giant government warehouse amongst countless similar crates.
- Ash Ketchum, Misty, Brock, Pikachu and Togepi will be guest stars in this film