In the opening scene, Jupiter Jones (Mila Kunis) begins by talking about her parents. Her father was a Russian named Maximilian Jones (James D'Arcy). Maximilian met and fell in love with a woman named Aleksa (Maria Doyle Kennedy). They watch the stars together through his telescope.
Later on, the two are expecting their child, which Maximilian wants to name Jupiter. Aleksa isn't too fond of the name. Two robbers break into the couple's home, and Maximilian gets shot. He dies in Aleksa's arms. Later on, Aleksa gives birth to Jupiter as she and her family are on a boat heading to America.
In the present, the adult Jupiter works as a janitor living in Chicago with her roommate Katharine Dunlevy (Vanessa Kirby). Jupiter hates her job and life, yet she is not very ambitious or eager to do anything else about it.
Three intergalactic bounty hunters - Falque (Spencer Wielding), Razo (Doona Bae), and Ibis (David Ajala) - are scoping out Jupiter's apartment.
The bounty hunters spot a man named Caine Wise (Channing Tatum) near the area. They realize that he is after Jupiter as well, and they go after him.
Caine realizes he is being stalked, and he emerges from the building with his hover boots, defending himself with his shield and shooting back at the bounty hunters as they attack him. He flees the scene unharmed.
Jupiter has dinner with her family and asks her uncle Vassily (Jeremy Swift) for money. He refuses to give her money and makes a rude remark that Jupiter is too smart for her own good and that's why she is unable to find a husband. Aleksa defends her daughter angrily, though the rest of the family seems to agree with Vassily.
Later, Jupiter is looking at a telescope on eBay. Her cousin Vladie (Kick Gurry) comes in and suggests she go to the fertility clinic and donate her eggs for some money. Jupiter agrees.
In space, the Abrasax siblings learn of Jupiter's existence. Their mother has died, and they now seek to inherit the earth as their own. Balem (Eddie Redmayne) awakens from a slumber after going through a successful planetary harvest.
His brother Titus (Douglas Booth) is cavorting with other women in his lavish castle, while his aide Famulus (Gugu Mbatha-Raw) informs him that Caine, who has been sent by Titus, has located Jupiter. Kalique Abrasax (Tuppence Middleton) also has concerns over the inheritance of the earth.
At the apartment, Katharine is getting ready to go out. A group of alien creatures called Keepers appear in the apartment and incapacitate Katharine. Jupiter takes a picture of them with her phone, and they lunge at her. Moments later, Katharine wakes up, and neither her nor Jupiter seem to know what just happened.
Jupiter goes to the clinic under Katharine's name, which Balem is informed of. He orders his people to find Jupiter and kill her. The doctors put her on the bed and then levitate her. They probe her and know Jupiter's identity, and they attempt to kill her.
Caine bursts in and kills the doctors as they reveal their Keeper form. He gets Jupiter out of there.
Jupiter finds herself atop the Willis Tower. Caine explains to her that he is a genetically-engineered being made up of a splice between a human and a wolf. Jupiter asks why she was almost just killed, and Caine tells her that she is the rightful owner of the planet. He claims that human life began not on Earth but on another planet called Orus. Jupiter also has no memory of the Keepers finding her and her taking a picture of them, which Caine explains as them erasing her memory.
They are beamed up by a spaceship hovering over them, when the bounty hunters show up and destroy the ship. Caine carries Jupiter as they fly over the city with his hover boots as the bounty hunters chase after them. Jupiter falls in the attack, but Caine catches her before she hits the ground. Caine hijacks a small ship and escapes with Jupiter.
Caine and Jupiter drive away from the city, where Caine continues to explain the Abrasax family history. They have been splicing humans with other animals for ages, and are responsible for events such as the extinction of the dinosaurs.