The film starts with a montage of a space station being built over many decades. By 2020, the station, Alpha, has become a center for different species from infinite planets to gather peacefully. However, Alpha is also a threat to Earth due to its massive size, which brings it closer to Earth's atmosphere. The President of the World State Federation (Rutger Hauer) delivers a message to those going on the journey to send Alpha further out into space.
400 years later on the planet Mul, Princess Liho (Sasha Luss) wakes up and greets a small creature called a converter. She steps out of her home to the beautiful surroundings in her world. The other Mul inhabitants, called Pearls, gather...pearls that they feed to other converters, which they then reproduce to give back to nature. Emperor Haban-Limai (Elizabeth Debicki) picks out a pearl especially for Liho. As Liho is admiring her home, multiple ships start breaking through the planet's atmosphere and come crashing down. The people of Mul rush to a survival fortress as the ensuing explosion starts to engulf the planet, but Liho fails to make it in before the door is shut and the handle gets broken. Haban looks at his daughter through the glass with remorse while his wife and Liho's mother Aloi (Barbara Weber Scaff) wails with sorrow. Liho turns around to embrace the explosion as her body explodes and sends a wave throughout the galaxy.
This wave hits Major Valerian (Dane DeHaan), who believes he was having a dream about Mul. He is on a beach (a simulation) with his partner/girlfriend Sergeant Laureline (Cara Delevingne). They tease each other and play-fight, though Laureline reminds Valerian that today is her birthday. They are then called upon to handle a mission. As they walk to their ship, Valerian continues trying to make things more serious between him and Laureline, but she is aware that Valerian has a long list of conquests, and she doesn't want to end up on that list.
The two fly to the planet Kyrian dressed like tourists to blend in with civilians. Valerian is to head into the market where tourists use devices to simulate a market setting. Before heading off, Valerian asks Laureline to marry him. She says she'll think about it.
Valerian meets with another agent who gives him a mechanical box to wear on his arm as he goes to retrieve a special item while Laureline works in the background to make sure Valerian finishes the mission. He enters the market and comes across a meeting between two Pearls, including the Emperor's son Tsuuri (Lee Delong), and Igon Siruss (John Goodman), a notorious wanted criminal. The Pearls want a converter that Igon has in his possession. They try to trade using one of their pearls. Igon takes the pearl and intends to rip them off, leading to a stand-off. Valerian shows up in the nick of time to stop Igon and take the converter and the pearl.
As Valerian is trying to head back, the box on his arm attracts dozens of small magnetic balls that cause him to fall many levels below the market. He meets a small alien child and upsets him in front of the boy's angry mother. Valerian runs away before the mother can get him. He runs to rejoin his team, but Igon has unleashed his pet beast to go after Valerian. He runs away and finds Laureline, but the beast breaks out and chases the team. They board their tour bus to head back to the ship, and the beast tears through the bus. Valerian and Laureline board their ship, and the beast hops on as well. The two fly high enough to send the beast falling back to the ground.
Valerian and Laureline report to Alpha with the converter. They meet with Commander Arun Filitt (Clive Owen), who tells them that there is an infection within the station that could spread within weeks. A number of soldiers have gone to see what the problem is, but they all turned up dead. Valerian and Laureline are assigned to protect Filitt. He requests to see the converter, but Laureline holds onto it.
When everyone else is gone, Filitt goes to a containment room where they are keeping a Pearl captive. The Pearl looks badly beaten. Filitt tells his men to continue trying to get information from the Pearl.
Filitt gathers everyone from the council together to report on the infection in Alpha. They are interrupted when a group of Pearls storm the room and trap everyone in blue shells. With everyone incapacitated, the Pearls take Filitt. Valerian cuts through his shell with a special mechanical spider he kept, and he goes to free Laureline. Valerian pursues the Pearl craft heading through Alpha. It moves closer and closer to the infection until Valerian goes so far that he loses contact with Laureline.
Laureline tries to get back in touch with Valerian, but to no avail. She is approached by three bird-like aliens called the Doghan-Dagui, who offer a solution to help her find Valerian. They find a pirate named Bob (Alain Chabat) and pay him to take them to find a quartex jellyfish. They find the jellyfish and have Laureline put it on her head so she can track Valerian.
Laureline locates Valerian and his crashed ship near the infected part of Alpha. Laureline then looks up and sees pretty-looking butterflies, but they turn out to be bait as it grabs Laureline's arm and pulls her up to the edge where large aliens are taking people. Valerian gets himself pulled up and he blows the head off one fisher. Laureline is then taken away.
Valerian goes to look for Laureline and ends up in a sketchy part of Alpha which is populated by crooks and sex workers. He gets invited into a club run by a pimp named Jolly (Ethan Hawke). He brings Valerian to the stage to watch the main attraction, a shapeshifting dancer named Bubble (Rihanna). After watching her mesmerizing performance, Valerian asks for Bubble's help in getting Laureline back. A minor incident occurs where Valerian's gun falls out and he must incapacitate Jolly when he pulls his own gun out. Bubble then joins Valerian.
Bubble helps herself and Valerian get in disguise as they find Laureline being brought as a sacrifice to a larger alien king. She is forced to wear a weird hat as the alien king prepares to scalp her, but Valerian and Bubble intervene. They fight and kill the king and his minions. Valerian goes to Laureline but they are attacked by another group of aliens. They escape down a vent with Bubble, but Bubble has been mortally wounded in the chaos. As she dies, Valerian tells her she was the greatest performer he ever saw. Her body then turns to dust.
Valerian and Laureline travel further within Alpha until they find a room where they see a whole group of Pearls, with Emperor Haban and his wife there. As the two demand answers, Haban tells them that Mul's destruction was 30 years earlier as a result of Filitt carrying out an order to strike the planet with a doomsday weapon, and the survivors made it out by hiding in a wrecked ship. They learned that they can rebuild their world with a pearl and a converter, which both Valerian and Laureline possess. The reason that Valerian has been seeing the Pearls in his head are because he has been possessed by Liho's spirit, which Haban tells him. Laureline convinces Valerian to give them the converter, despite the orders having been to hand it over to their superiors. Using the pearl, the Pearls recreate Mul as a simulation within their ship.
Valerian and Laureline confront Filitt, who claims he did what he did for humanity, but he has also been trying to keep his war crimes a secret by trying to eliminate the Pearls. In truth, he wanted their pearls and destroyed Mul when the Pearls wouldn't give them up. Outside their ship, Filitt's subordinates stand outside waiting for a command. Filitt orders his K-Tron robot soldiers to fire. Some Pearls and soldiers are killed, but Valerian destroys the K-Trons and has Filitt tied up. Filitt is exposed for his crimes and is arrested.
The Pearls are thankful to Valerian and Laureline for giving them their home back, and Haban tells Valerian that Liho can now rest in peace. Valerian and Laureline are ejected from the ship in a shuttle, with a rescue team arriving in a few hours. Valerian once again proposes to Laureline with a Mul pearl. He promises she will be the only one on his list. The two of them kiss.
*CUT TO THE CHASE*
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The space station Alpha is home to millions of inhabitants from different races and species from all over the universe. Valerian and Laureline are agents working for Alpha, and they come across a dark secret.
Valerian finds a pearl and a creature called a converter, both coming from the destroyed planet Mul. The planet's inhabitants, the Pearls, kidnap Alpha's Commander Arun Filitt, forcing Valerian and Laureline to go rescue him. During their mission, they meet other alien creatures who help the or try to kill them.
Upon meeting the Pearls, Valerian and Laureline learn that Filitt carried out the destruction of Mul for trying to obtain Mul's pearls. He attempts to kill everyone in an attempt to cover up his secret. The heroes thwart his plans, and Filitt is arrested.
The Pearls recreate Mul using a pearl and a converter to form a simulation of the planet. Valerian and Laureline express their love for each other and get engaged.
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