Around 1400 BC, after the Ten Commandments were smashed by Moses, the pieces were collected in the Ark of the Covenant, a gold-gilded wooden chest constructed under instruction from God and carried before the Hebrews on their march towards the Promised Land.
When the Hebrews settled in Canaan, they placed the Ark in the Temple of Solomon where it stayed until around 980 BC when the Egyptian Pharaoh Shishak raided the Temple and took the Ark with him to the city of Tanis. Following a series of dreams in which he was visited by Osiris urging him to hide it from the eyes of the sun god Amun-Ra, Shishak had the Ark placed inside the Well of the Souls. A Map Room was built so that only Ra could know the Ark's whereabouts but a year later the Israelites' God saw to it that Tanis itself was buried in a sandstorm and the Ark was lost to the passage of time.
Adolf Hitler became interested in acquiring the Ark and its fabled powers in order to achieve world domination. In 1936, when US agents Colonel Musgrove and Major Eaton discovered Hitler's plan through an intercepted German communique sent from Cairo, they consulted Indiana Jones and his friend Marcus Brody about the artifact. Jones explained some of the history of the Ark to the government men, showing them a depiction of the Ark's destructive power after which Brody noted that any army which carried the Ark before it would be invincible. Eaton and Musgrove subsequently hired Jones to find the Ark before the Nazis. Although the archaeologist managed to acquire the Ark out from under the German expedition, it was later captured by Nazis nonetheless.
The Ark changed hands between Indy and the Nazis several times before the Nazis took the Ark to a secret island base near Crete. After René Emile Belloq performed a Hebrew ritual, the Ark was opened. Inside was sand, all that was left of the Ten Commandments. While Belloq looked upon the sand with an anguished expression on his face, a sudden screeching noise drew his attention. Moments later, a power surge from the Ark disabled all the lights, electronics and weapons in the vicinity, some blowing up in the soldiers' hands.
Ghostly apparitions emerged from within and swarmed playfully about the Nazis before adopting a more sinister tone; the spirits transformed their appearances from angelic beings into monstrous demons. Rooted to the spot with fear, the Nazis beheld a pillar of holy fire rising from the Ark and coalescing around Belloq before shooting bolts of fiery energy through the assembled soldiers, killing them. The Ark then turned its full and terrible wrath onto Belloq and his cohorts: Colonel Herman Dietrich's head imploded, Major Arnold Ernst Toht's face melted off his skull and Belloq's head exploded. The Ark then swept their remains into the air to have their souls judged, then fire shot the cover into the sky before it fell back onto the Ark. The captured Indy, witnessing energy beginning to come out of the Ark, realized what was about to happen. Warning Marion Ravenwood, they closed their eyes and looked away from the Ark, symbolically showing proper respect, and were spared from the wrath of God.
Afterwards, instead of giving the Ark to the National Museum as agreed, the US government took possession of it. Though Jones and Brody were told by Major Eaton that it was to be studied by higher authorities, the relic was simply nailed inside a wooden crate numbered 9906753 and placed inside a gigantic warehouse among hundreds of similar crates.
Two years after discovering the Ark, Jones later uncovered a wall painting depicting the Ark in some tunnels beneath the Biblioteca di San Barnaba in Venice. When Elsa Schneider asked what the image was, Jones confirmed that it was the Ark, mumbling that he was "Pretty sure..." given past encounters.
Over two decades later, in 1957, Jones was taken to the warehouse when captured by Soviets looking for a different crate. The box containing the Ark was broken during the subsequent action, but the preoccupied Jones and his pursuers did not notice it.