Young Indiana Jones and his Scout troop are on a trip through the Utah desert when Indiana stumbles across some grave robbers who've uncovered the Cross of Coronado. So, you know, it's just your average 1912 Boy Scout field trip.
Indiana steals the artifact and outsmarts the grave robbers but is ultimately forced to return the cross to them by the local law enforcement. Fast forward to 1938, and Indiana gets the last laugh when he once again steals the cross and donates it to Marcus Brody's museum.
After ducking out of office hours at the college where he teaches, Indiana's picked up by a car full of shady dudes and taken to meet Walter Donovan. Donovan tells him that Indiana's dad has gone missing while trying to locate the Holy Grail. Indiana enlists the help of Brody and, guided by his dad's Grail diary, the two men set out to find Indiana's father, Henry.
In Venice, they meet Dr. Elsa Schneider, Henry's partner in the Grail quest—and the last person to see him alive. Using Henry's Grail diary as a guide, Indiana and Elsa investigate the catacombs beneath the library and find a clue to the Grail's location. They also find themselves being pursued by a band of men who've sworn to protect the Holy Grail.
The chase moves from the catacombs to speedboats, and Indiana ultimately captures one of the men, Kazim, who tells him that Henry's shacking up (against his will) at Castle Brunwald. Indiana and Elsa take off for Germany, but not before giving Brody a map to the Grail from Henry's diary for safekeeping.
Indiana infiltrates Castle Brunwald by impersonating a Scottish lord. When Indiana breaks into Henry's room, Henry, in turn, breaks a vase over his son's head, mistaking him for one of his captors, and is more worried about the potentially priceless vase than he is about Indiana's noggin. Classic dad.
Then the Nazis burst in, and it's revealed that Indiana brought Henry's beloved Grail diary with him—as in, right into the hands of the enemy. As if that weren't bad enough, they also find out that Elsa and Donovan are working for the Nazis and plan to use the Joneses to help them secure the Grail. Oops.
Indiana and Henry try to flee Germany, first on a zeppelin, then on a biplane. They succeed, but only after a shootout with flying Nazi goons. Meanwhile, Brody gets captured in Iskenderun while trying to meet up with his and the Jones' old pal Sallah. That means the Nazis have the map to the Grail, and they waste no time in trying to track it down.
The Joneses catch up with the Nazi caravan, which includes a tank, trucks full of Nazis, and Donovan's sadistic right-hand man, Colonel Vogel. Kazim and his men show up and enter the fight, as well, only to get killed. Henry's captured in the fray, but ultimately Indiana saves both Henry and Brody by fighting off waves of Nazis, including Vogel, who rides that gnarly tank we just mentioned off a cliff to his death.
For a moment, Henry believes that Indiana met a similar fate, and he laments that he didn't have just a little more time with his son. When Indiana shows up, alive and well, he and Henry hug it out. Then Indiana collapses, and Henry chews him out for taking a break when they're so close to the end of their quest.
Indiana, Henry, Brody, and Sallah find Donovan and Elsa in the temple where the Grail's located. It's protected by three obstacles that each require a healthy dose of brains, guts, and faith. Donovan shoots Henry in the stomach, forcing Indiana to go for the Grail—because if somebody doesn't get Henry a Holy Grail full of H20, he's going to kick the bucket.
Indiana passes all three tests and finds a room full of grails guarded by one seriously old knight. All Indiana needs to do is choose the correct cup, and he can use it to save his dad. If he chooses the wrong cup, both he and his dad will die.
Just then, Donovan and Elsa show up. Donovan cuts ahead of Indiana, and chooses a cup. He chooses poorly and dies a quick but thoroughly nasty death. Indiana chooses the right cup and uses it to save Henry. Elsa then tries to take the Holy Grail out of the temple, which the old knight told them was a huge no-no.
The temple begins to shake, quake, and collapse, and the Grail tumbles into a giant crack in the floor. Elsa falls to her death trying to grab it. Indiana's also momentarily blinded by desire for the Holy Grail and immortality, but Henry snaps him out of it, telling his son to let it go. Indiana drops his Holy Grail dreams and his resentments toward dear old Dad, and the Joneses leave the Grail in the temple where it belongs. Then they (literally) ride off into the sunset with Brody and Sallah.