Deciphering the description on the staff headpiece, Indy and his team find that the Nazis are digging for the Ark in the wrong location. Sneaking into a tiny map room, Indy uses the headpiece and proper size staff to find the correct location of the Well of Souls.
Indy and Sallah begin digging and retrieve the Ark - but Belloq finds them in time. His team surrounded, Marion is thrown into the sunken tomb with Indy, and the entrance is sealed. Snakes then slither through openings in the walls. And Indy hates snakes.
Mr. Jones climbs a huge dog/human statue, and rocks back and forward until it breaks from its foundations to smash through a side wall, hiding a bunch of ancient dead bodies. Indy and Marion escape through some shoddy masonry work to an airfield, but Indy gets into a fight with a huge German. The German meets a sticky end with a propeller, while Marion goes crazy with the plane's machine gun and takes out the fuel dump to aid their getaway.
Belloq and his team take away the Ark in an armoured convoy. Giving chase on horseback, Indy takes out the soldiers one by one (in a friendly way by throwing them to the road), although is shot by a persistent German Crocodle Dundee in the arm. Indy finally manages to capture the truck carrying the Ark and shunts Belloq's car off the road.
Using a contact of Sallah, Indy and Marion board a cargo ship with the Ark still in its crate - but a German U-boat stops the ship and its crew take off the crate, and capture Marion. They cannot find Indy - the Captain tells them that he has already been killed. As the U-boat is about to dive, Indy swims over to hitch a ride.
When the sub arrives at its destination, Indy is out and steals a guard's uniform. They all start a long trek up a sandy mountain. Indy sneaks away from the column and takes out a rocket launcher - threatening to blow up the Ark - but Belloq knows that, as an Archaeologist, he is lying. Indy is soon captured.
At a big faux-Jewish ceremony at the top of the mountain, Indy and Marion are tied to a pole and forced to watch. Belloq leads the event, and opens the Ark - to find sand inside from the old Tablets. Suddenly a mystical force is awakened. The lights go out. Indy tells Marion to close her eyes, and keep them closed.
Lost souls fly about the watching Nazis - but then turn nasty. Fire erupts from the Ark, through Belloq, and then into each soldier's heart. It burns the face of the nasty little HairFlick Gestapo character and then the others - and the rushing fire then reaches up to Heaven and back - the lid falling back into place on top of the Ark. Indy and Marion survive.
Indy and Marcus are back at the University. The Government tell the pair that the Ark is in safe hands in a secure facility. Marion takes Indy off for a drink.
Meanwhile the Ark is locked away in a crate and hidden in an anonymous large warehouse with thousands of other crates, not to be seen again until ... the terrible 4th film in the installment that should never have been made. Or just plain made a whole lot better.