The Tanis digs, marked by excavation platforms and equipment, are swarming with Nazis and hundreds of Arab workers. Belloq pursues a frustrating search for the Well of the Souls on a ridge-top. Disguised as Arabs, Sallah and Indy stealthily move toward the map room a short distance away, where the sun will be perfectly positioned at about nine in the morning. In the center of a mound of dirt is a circular hole/entrance - an open skylight high above the map room.

Indy descends into the map room on a long length of rope. Their plan is that Sallah will immediately pull him up when he tugs on one end of the rope. At the far end of the beautifully decorated room - with walls covered by carvings and frescoes - is an elaborate relief map. It shows a miniature stone model or replica of the ancient city of Tanis. A beam of sunlight from the skylight floods the room with a stream of light. As Indy surveys the map room below, Sallah is mistaken for a servant by the Germans and the rope is confiscated. He is detained next to a jeep, a short distance from the mound.

In the map room with little time left to spare before nine A.M., Indy brushes off dirt from the mosaic base line for the staff. He deciphers and calculates from the stone inscription hieroglyphics on the floor where the staff must be positioned. He attaches the headpiece at the top of the Staff of Ra and places the staff's base in the correct depression on the baseline. In a transcendent, exciting moment, the sunlight moves along the wall and floor and then catches the top of the headpiece. As the ray of light shines through, it is magnified and sends a tiny beam of light toward one building in the miniature city. The focused light causes an intense, searing glow to flood the scene. It marks the proper location of the Well of the Souls - a different spot from where the Nazis are digging. After breaking the wooden staff in two, Indy calls for Sallah to throw down the rope from the skylight. Sallah, who has eluded the Nazis, rescues Indy with a makeshift string of clothing - the first section of which is a bright red Nazi flag.

When the two begin walking out of the camp, they must avoid Nazi confrontations. While Sallah retrieves water for demanding Germans eating lunch at a table, Indy ducks into one of the tents' openings and finds Marion gagged and bound to a tent pole as a hostage. He is relieved to realize that "they must have switched baskets." As Indy pulls out his knife to cut her ties, he suddenly stops when he realizes that if she is freed, the Nazis will find her gone and his presence at Tanis will be detected. They would comb the place for both of them and interrupt his obsessive search for the Ark. He replaces the gag back on her mouth, as she protests, kicks, and screams at him. He kisses her on her forehead and promises: "I'll be back to get ya," and then hurries out of the tent. Using a surveyor's instrument on a high sand ridge, Indy uses his readings to view the virgin spot in the sand where he must begin digging.

High-ranking Nazis are becoming exasperated and impatient with Belloq. They suggest that "the girl" (to whom he takes a protective fancy), who was in possession of the original medallion for years, may be able to help them. Toht also reappears - his crisp "Heil Hitler" salute reveals that his palm is scarred and burned with the exact imprint of the medallion.

With help from a small band of Sallah's diggers, Indy begins the work of excavating the new location nearby. After the bright red sun sets, ominous storm clouds appear and lightning flashes. The storm intensifies when the diggers hit stone - part of the heavy entry door to an underground chamber, the Well of Souls. Crowbarring the edge of the slab open, they unearth the historic tomb. Holding torches, Jones and Sallah peer into the asp-ridden cavern where they see the face of a dragon statue. Then they stare back into the chamber:

Sallah: Indy, why does the floor move?
Indy: Gimme your torch. (Indy throws a torch down into the thirty foot deep chamber where it hits the floor. Hissing noises arise.) Snakes. Why'd it hafta be snakes?
Sallah: Asps. Very dangerous. You go first.

More torches are thrown in the chamber to create a clear, snake-free area on the floor - the snakes hate fire.

The scene of the unearthing of the chamber and discovery of the ark is cross-cut with the scene of Belloq's attempted seduction of Marion to find out about the location of the Ark. After being untied, Marion runs for the tent entrance to escape, but is told that she would be foolish - the desert is three weeks distance in every direction. From a tray of food, Marion begins to eat and then she is entertained by Belloq, who offers her a new white dress and shoes to wear. He slyly watches her disrobe through a small mirror reflection.

As he attempts to get information from her regarding the location of the ark, she also attempts to lure him into a drinking contest while covering a knife that lies on the table. They both become very drunk. (Belloq has a high tolerance for the alcohol, claiming he grew up on the stuff - his family label.) They laugh uproariously when she pulls a knife on her captor. When she attempts to back out of the tent, she is halted by the sudden appearance of Toht, who threatens her: "We meet again, Fraulein. You Americans, you're all the same with overdressing for the wrong occasions." The sadistic German takes out an evil-looking chain device that looks like a weapon - it is actually a coat hanger. He sits down across from Belloq and Marion and asks: "Now, what shall we talk about?"

Indy carefully lowers himself into the chamber, but falls to the floor where he lands directly face-to-face with a flaring cobra in an excruciatingly horrific moment. [Visible is a piece of plexiglass that separates Harrison Ford from the lethal snake.] Indy sprays kerosene from canisters onto the snakes, and then ignites many of the snakes with his torch. Sallah and Indy approach a stone altar/platform at the far end of the underground chamber. Pushing together with all their strength, they remove the top of the large protective stone chest that encloses the Lost Ark. Fitting wooden poles through the rings on the side of the Ark to avoid touching it, they lift the Ark clear of its stone chest. It is awesomely beautiful - a gold-overlaid rectangular box, with two sculptured gold angels mounted to face each other on top.

At sunrise, the Ark is placed in a wooden crate, and then hauled up to the surface with ropes. (Meanwhile on a nearby ridge, Belloq notices the digging and discovers their alternate site.) The torches have begun to burn out and the snakes move menacingly closer. Sallah climbs out of the chamber on a rope, but the exit rope for Indy drops loosely at his feet. Looking up, Indy sees Belloq (with his Nazi men) staring and waving to him from the opening above:

Belloq: Why, Dr. Jones, whatever are you doing in such a nasty place?
Jones: Why don't you come on down here, I'll show ya.
Belloq: Thank you, my friend, but I think we are all very comfortable up here...So once again Jones, what was briefly yours is now mine. What a fitting end to your life's pursuits? You're about to become a permanent addition to this archaeological find. Who knows? In a thousand years, even you may be worth something.

Refusing to pull Jones from the tomb to safety, Belloq instead has Jones entombed alive. Before the lid is lowered on the tomb, however, Toht pushes Marion into the hole to be sealed inside the Well of Souls with him. (Belloq is distressed and yells "No!" when Marion joins Jones in the tomb, and bids her a sad farewell.) Her fall is partially broken when she catches hold of the dragon statue midway and she drops into Indy's arms. Her weight causes him to fall to the ground and almost into the snakes. After Belloq bids them 'adieu,' the evil Toht giggles as he walks away from the tomb. Marion's scream of "Nooooo!" is cut off sharply as the tomb is sealed up, and both Belloq and Sallah cringe in horror and shut their eyes.

When the heavy stone door seals the chamber, the torches inside the tomb begin to extinguish themselves due to lack of oxygen. Indy hands a torch to Marion, instructing: "Wave it at anything that slithers." Indy also questions her about the dress she is wearing and wonders aloud how hard she was really trying to escape.

Examining the walls and seeing snakes slithering out through holes, Indy figures that the secret chamber is probably connected to other chambers already excavated by the Nazis. He has a brilliant idea - he climbs up one of the pillar columns/statues and braces himself between the tall pillar and the top of the chamber and then pushes against it with all his might. After rocking it, the pillar breaks loose and falls like a tree as Indy rides on top of it. It smashes through the chamber wall, just as the last torch burns itself out.

More horrors are revealed in the pharaoh's tomb on the other side of the broken wall. It opens into catacombs full of cascading, moldering mummies, sarcophagi and skulls (one has a snake slithering out of its mouth). A nervous wreck, Marion thinks Indy hasn't survived. But then, she is grabbed by Indy as he shows her their exit - a crack in the corner of the chamber through which sunlight beams. Once they miraculously make their way into the daylight from the abandoned excavation, as luck would have it, their escape occurs above an improvised, crude desert airstrip serving the digs. The two are within sight of the Flying Wing airplane with twirling propellers that will soon carry the Ark to Hitler. First crouching under its wing near the plane, Indy quickly subdues a monkey wrench-wielding German mechanic. Then he faces a second, burly, bald and shirtless opponent.

In an exciting sequence, the two fight and punch at each other as the plane's pilot tries to get a clear shot at Indy from the cockpit. Marion bashes the pilot (Frank Marshall, the producer of the film in a bit part) over the head, and knocks him into the throttle. His weight revs up the plane, causing it to rotate in a circle around one set of blocked plane tires. The plane's cockpit cover shuts above her, but she is able to take over the plane's machine gun. On the tarmac, the two opponents continue to fight within inches of the plane's lethal propeller blades. Marion's gun fire punctuates refueling tanks. Spilled fuel floods the entire area and quickly catches fire. Soon, the burning fuel will ignite the fueling truck and the airplane.

The big German doesn't see the spinning, whirring blades roar toward him from behind. The propellers hack him to death - a red spray of blood covers everything (the cockpit window and the Nazi flag) to register his offscreen demise. Indy frees Marion from the cockpit and runs from the flaming scene to safety. When the entire plane explodes in a huge fireball, Belloq senses that "Jones!" was responsible for the massive destruction. One of the Germans orders the Ark loaded aboard a truck to be driven to Cairo and then flown from there to Berlin. Sallah tells them about the new course for the Ark:

Sallah: Indy, you have no time. If you still want the Ark, it is being loaded onto a truck for Cairo.
Indy: Truck? What truck?

From a nearby hillside, Sallah, Indy and Marion watch the crated Ark as it is placed inside the back of a canvas-topped truck. Nazi guards protect the truck in a caravan, with Belloq in a staff car in front of the convoy. Indy thinks hard about what to do next in this unpredictable situation:

Indy: Get back to Cairo. Get us some transport to England. Boat, plane, anything. Meet me at Omar's. Be ready for me. I'm going after that truck.
Sallah: How?
Indy: I don't know. I'm making this up as I go.

From among one of the tents, Indy suddenly bursts into view atop a magnificent white Arabian stallion (as a classic western-style hero), and gallops off across the desert in pursuit of the truck.

Jones' impromptu chase is one of the most exciting chase sequences ever filmed, similar to Westerns with runaway stagecoaches. He cuts cross-country to catch up with the convoy that appears in view far below him. He follows along on a parallel ridge, and then descends to the road to ride alongside one of the trucks. He leaps from his horse onto the rear of the canvas-topped truck, tosses the guard from the passenger seat, and begins grappling with the driver. After negotiating some difficult steering, terrain, and obstacles in the path, Indy tosses the driver out and takes control of the wheel.

During various stages of the chase, Indy forces several escort vehicles off the road. After some unsuccessful, but hair-raising attempts of Nazi guards in the back of his truck to oust Indy from the wheel, he is weakened when one guard shoots him in the left arm. The last remaining guard reaches the truck's cab from above. Indy is tossed through the windshield and ends up hanging from a hood ornament in the front of the fast-moving truck. When the ornament bends and cracks off, he grabs onto the grill. The grill bars snap one by one and Indy clings to the fender of the front tire.

To avoid being rammed in the back of the car ahead, Indy lowers himself under the engine where he clings tenuously beneath the vehicle. He makes his way to the truck's rear wheel axle - he even gets dragged behind the truck while attached by his bullwhip. Eventually, he pulls himself forward and lifts himself up onto the rear of the truck, crawls back in, works his way back to the cab, and jumps into the driver's cab. Angered, he throws the driver out through the already-broken windshield. With the situation reversed, the Nazi cannot duplicate Indy's acrobatics and is crushed to death.

Just outside of Cairo, Indy forces the staff car off the road and sends it down an embankment. Indy's interference causes Belloq to curse his own driver: "Idiot. Idiot." Then, Indy speeds off toward Cairo, enters its narrow streets, and drives into a gaping garage opening in the center of Omar's Square where Omar, Sallah and his men are waiting to hide it. Indy conceals the truck in Omar's garage, covered by tenting. The truck and garage are further hidden by a hastily-assembled mini-bazaar of Omar's and Sallah's friends. When the Nazi staff car pulls up, they desperately look for the truck but cannot locate it - the Ark has been successfully recaptured. Sallah informs Indy of the next step:

Sallah: Everything at last has been arranged.
Indy: The Ark...
Sallah: ...is on board. Nothing is lacking now that you are here, or what is left of you.

A trustworthy, black ship captain named Mr. Katanga (George Harris) has been commissioned by Sallah at the Cairo waterfront docks to take the wounded Jones and Marion (and the Ark in the cargo hold) in an old tramp steamer named the Bantu Wind to England. When Marion says goodbye to Sallah, she gives him a kiss each for Fayah, his children, then for himself (on the lips). A delighted Sallah walks away singing "A British Tar Is a Soaring Soul, As Free as a Mountain Bird..." from Gilbert and Sullivan's HMS Pinafore.

On board, Marion appears in a white, silky nightgown lent to her by Katanga: "I've got a feeling I'm not the first woman to travel with these pirates." While they both look at themselves at opposite sides of a mirror, Marion flips it up and slams the mirror into Indy's face. A cutaway to the exterior of the steamer accentuates the echoing volume of Indy's scream. Marion and Indy have a short while to rekindle their romance in the film's only 'love' scene, but Indy is suffering in pain:

Marion: You're not the man I knew ten years ago.
Indy: It's not the years, honey, it's the mileage.

Indy tells her that the only place it doesn't hurt on his body is his left elbow. She kisses it for him and he prompts her to continue kissing him - on the forehead next, then on his right eye and his lips. But he soon falls asleep as Marion ponders: "We never seem to get a break, do we?"

In the hold, the ship's rats are nervous and agitated by the crate holding the Ark - it hums loudly, and the Nazi swastika symbol on the crate's surface is scorched. The couple's bliss is short-lived. By the next morning - Indy thinks something is wrong when the ship turns quiet and its engines have stopped. He loads his gun and goes on deck to check out what is wrong.

A German submarine [the same model used in the German U-boat film Das Boot (1981)] has overtaken the steamer and is sending over a boarding party. The Nazis quickly take over the ship, herd the pirates on deck, repossess the Ark, and seize Marion from the cabin.

Jones cannot be found as he manages to hide in a funnel while the steamer is searched - Katanga tells the Germans an alibi: "Jones is dead." Desiring Marion once again, Belloq angrily demands to take her: "The girl goes with me. It will be part of my compensation. I'm sure your Fuhrer will approve."

As the German submarine sails away, Jones is viewed clinging to the top of the vessel. The submarine is sailed to a mysterious island in the middle of the Aegean Sea, somewhere southeast of Greece (the journey is superimposed on a map), where a Nazi base has been built in its hollow interior. Jones disguises himself as a Nazi soldier after being forced to knock out a second soldier to get a properly-fitting uniform. Before sending the Ark to Hitler, Belloq explains to the uncomfortable German commandant that it must first be opened in a preliminary ceremony on a secluded part of the island:

Would you be more comfortable opening the Ark in Berlin - for your Fuhrer - finding out only then if the sacred pieces of the Covenant are inside? Knowing only then, whether you have accomplished your mission and obtained the one, true Ark?

Jones follows alongside Belloq's men, as the Ark is marched into a rocky cavern on the island. Indy ducks out of sight when no one is looking, climbs the cavern wall, and halts the procession from the cliff ridge with a bazooka on his shoulder. His weapon is aimed directly at the Ark as he shouts:

Indy: I'm going to blow up the Ark, Renee.
Belloq: Your persistence surprises even me. You're gonna give mercenaries a bad name.

Threatening to destroy the Ark unless Marion is released, Belloq refuses to be bluffed by Indy and appeals to the archaeologist in Indy:

Blow it back to God. All your life has been spent in pursuit of archaeological relics. Inside the Ark are treasures beyond your wildest aspirations. You want to see it opened as well as I. Indiana. We are simply passing through history. This, this is history. Do as you will.

Rather than risk Marion's life once more, Indy lowers his bazooka and surrenders to them.

Now nighttime, Indy and Marion are tied back-to-back to a stake, and watching from a few hundred feet away as the Ark is ceremonially brought into a small grotto or crevice of rocks. Belloq, dressed in Hebrew robes, delivers a short Hebrew incantation over the Ark before it is ritualistically opened - he is greedy in the belief that the Ark will give him and the Nazis ultimate power. [Belloq's acquisition of 'Jewish' characteristics, and his frequent opposing nature to the will of the Nazis may be met with the punishment of death.] The momentous event is being documented by a film crew, and dozens of Nazi soldiers anxiously anticipate the removal of the Ark's lid.

The film's finale contains the most-remembered, intense scene of all when God's fiery vengeance is visited upon the Nazis. [The scene is reminiscent of the opening of the Great Whatsit box in the climax of Kiss Me, Deadly (1955).] When the gold lid is removed by two Nazi soldiers, Belloq reaches in to discover only fine grains of sand within. (Have the stone tablets of the ten commandments disintegrated?) But the Ark unleashes electrical energy and charges, zapping all electrical lights, apparatus and machines in the arena. Things turn dark, and then a loud humming noise emanates from within the Ark. Inside the box itself, there is a wondrous, brilliant light, and a white smoke undulates out of it and blankets the ground. Indy warns Marion to look away (similar to the Biblical story of Lot warning his wife not to watch the destruction of Sodom, or Adam and Eve's knowledge of the forbidden fruit and subsequent loss of innocence in the Garden of Eden):

Don't look at it. Shut your eyes, Marion, and don't look at it, no matter what happens.

Belloq has an obsessed, transcendent look on his face - he believes that the blinding light in the Ark is beautiful. Ghostly spirits hypnotically zoom around everyone - but apparently, God's wrath has been summoned, as the forms change from wondrous to deadly visions. Belloq is besieged by the ghostly images and screams in horror - the interlopers are punished by a lethal dose of death for breaking the sacred taboo. The villain is consumed by flames, and piercing firebolts and shafts of fire zap the rest of the Nazis through the heart. One firebolt actually travels through one of the movie cameras, destroying the visual evidence of the event! Toht's head, along with the heads of several other commanding Nazis, melts into dripping ooze by the extreme heat, while Belloq's head explodes.

The climactic firestorm creates a rushing vacuum of wind and a rising plume of fire above the island. Suddenly, the blinding fire in the heavenly sky reverses itself, and the fire is sucked and swallowed up by the Ark. When the forces are returned inside the Ark, the lid slams down tightly and neatly shuts and seals itself, and covers up the divine powers. Only Indy and Marion survive the holocaust because of their humility and reverence for the awesome forces.

At the film's end in the final scene back in Washington D.C., Indy is congratulated by two Army Intelligence Officers: "You've done your country a great service." However, Indy and Brody find the "situation totally unacceptable." Although told that the Ark is "someplace very safe," they are concerned about its storage and that the government doesn't understand that the Ark is "a source of unspeakable power." They are left with the vague promise that some of the government's unidentified "top men" are researching it: "We have top men working on it right now."

Emerging from the building, Indy tells Marion his frustration:

Fools, bureaucratic fools...They don't know what they've got there.

Marion responds with the film's final line: "Well, I know what I've got here. Come on. I'll buy you a drink. You know, a drink?" Indy has successfully fought and obtained the Ark, only to lose it in the end to the government. His instincts prove correct about the bureaucracy. The Ark of the Covenant is crated in a wooden box and its lid is solidly nailed shut. Its stenciled label contains a long inventory number for identification:

TOP SECRET, ARMY INTEL 9906753 DO NOT OPEN!

A warehouseman pushes the crated Ark down a long aisle formed by huge stacks of similar crates in an enormous government warehouse (a lengthy matte shot), where it will again be hidden away - presumably by bureaucratic inefficiency. The crate is summarily filed away in a scene deliberately reminiscent of one of the final scenes in Citizen Kane (1941). One might wonder, what are in the other crates -- other governmental bureaucracy secrets that are being deliberately withheld, hidden, possibly because of fear of misuse?

[In Indiana Jones and the Kingdom of the Crystal Skull (2008), the warehouse - revealed to be in Nevada - was revisited. The Ark itself was accidentally uncovered and visible during a scuffle with KGB agents, but went unnoticed by the combatants.]

Note: A spoof in MAD magazine in January, 1982 (entitled "Raiders of a Lost Art") commented ironically about the other crates in the warehouse, labeling them: "Clean Non-Polluting Stuff," "Long-Lasting Light Bulbs," "Synthetic Fuels," "Long-Lasting Soaps," "Break-Proof Toys," "Cancer-Proof Cigarettes," "Never-Die Batteries," "Safe Sugar Substitutes," "Fuel-Saving Automobile Engines," and "Efficient Solar-Power Cells."