Indiana Jones and the Saucermen from Mars was set to be the fourth film during the 1990s. It was scrapped and eventually elements of it were retained in Indiana Jones and the Kingdom of the Crystal Skull (the Nevada opening in particular).
After battling river pirates and a rival archaeologist, Indy and his friend Kabul stop at a local fishing port to pick up Dr. Elaine McGregor, a linguist, whom Indy has been hired to escort to a jungle temple. Indy is instantly smitten with the confident brunette, and through various adventures, the two rough-edged academics fall in love.
Back stateside, Indy and Elaine are about to tie the knot, despite barely knowing one another. Indy's former flames, Marion and Willie, his old friend Sallah, and Henry Jones, Sr. are there to witness an event they thought they'd never see. As Indy and his father stand at the altar waiting for Elaine to walk down the aisle, she leaves — still dressed in her gown — and hops in a car with a mysterious man.
A heartbroken Indy searches Elaine's office and finds clues that point to her going to the White Sands Proving Grounds in New Mexico, the military base where the Trinity nuclear bomb tests were held. Indy gets caught snooping around the base and is interrogated by Bob Bolander, the same man that took Elaine away from the wedding.
When Elaine is called to verify Indy’s story, she realizes she could actually use his help. Despite Bolander’s resistance, Indy is allowed to join a top secret project researching debris found at the crash site of a flying saucer. Indy is skeptical, but his interest is piqued when he's shown the charred remains of alien bodies, as well as a strange stone cylinder. The cylinder is covered in a series of rings and complex code written in ancient languages including early Egyptian hieroglyphics and Sanskrit. In addition, the cylinder is a great source of power, able to turn on a radio or illuminate a light bulb by proximity alone.
Thanks to a room-sized computer, Indy and Elaine crack the coded symbols on the cylinder. One section is latitude and longitude coordinates for nearby Mt. Keebo. Indy surmises that perhaps the aliens were trying to take the cylinder to the mountain when they crashed. The rest of the code seems to be descending numbers, like the countdown for a bomb. That can't be good.
Soon after, Elaine and the cylinder are taken and placed aboard a plane full of Russian spies. Indy tries to rescue her, but is about to be tossed out the bomb bay doors when a flying saucer appears and tries to take control of the plane. Its plan is foiled, though, when Air Force jets are scrambled, leading to a high-speed dogfight.
Later, our heroes have a close encounter of the third kind after their truck is lifted off the ground by a beam coming from the bottom of the saucer. When Indy approaches the aliens to return the cylinder, whose rings are now glowing because the countdown has begun, the aliens back away and keep saying, “Mukara. Mukara.” Being a linguist, Elaine realizes that Mukara is Sanskrit for “dangerous.”
Suddenly, explosions rock the area as Army tanks and missiles under the command of Bolander destroy the UFO. Bolander takes the cylinder and he and his convoy head towards Mt. Keebo. Indy and Elaine – as well as a Russian spy and a new flying saucer – give chase.
Just before going up the mountain, the Army attacks the flying saucer with everything they’ve got. But this time, when the shooting stops, the ship is unharmed. It begins to rise above the ridgeline and we see that it’s a gigantic mothership that fills the sky. Bolander hightails it in his Jeep, but the rest of the convoy is frozen in horror. The saucer is able to conjure up a great wind that sweeps through the valley, flipping trucks and tanks like a child’s toys, and burying men in the desert sand.
On Mt. Keebo, just before dawn, three saucers appear in the sky, each emitting a green light focused on the summit. Bolander takes the cylinder into the green lights and holds it above his head as his body surges with power. Suddenly, a bright white light shoots out of the cylinder. Bolander points it at the Russian, who melts before our eyes.
But then, the sun breaks the horizon, and it seems to invigorate the saucers, which glow brighter and brighter. Bolander holds the cylinder above his head again, hoping that its power will have some effect on the spacecraft. Instead, a beam fires out of the bottom of the cylinder, splitting Bolander in two. The cylinder’s white light becomes blinding, the hum of the saucers becomes deafening, and then, in a flash...the saucers and the cylinder are gone.
Back at home, Elaine and Indy finally get married with the same old friends in attendance. When they get in the car, a now grown-up Short Round drives the happy couple off into the sunset.
Behind the scenes
Lucas began writing the story in September 1993, and Jeb Stuart wrote a script (where Indy's love interest is named Molly, and Indiana has to protect a live alien). Stuart was replaced by Jeffrey Boam in 1995. The following year, Lucas and Spielberg (who already had troubles with aliens as the MacGuffin) decided the script was too similar to Independence Day, which was breaking box office records.
In Indiana Jones and the Kingdom of the Crystal Skull, Indiana Jones actually quotes the title, "Saucermen from Mars?" in the dialogue.