The film begins with a young Elio Solis, portrayed by Yonas Kibreab, visiting an air and space museum with his aunt, Major Olga Solis. Following the tragic loss of his parents, Elio has struggled to fit in with his peers and form meaningful connections. While exploring the museum, he stumbles upon an exhibit featuring the Voyager 1 spacecraft, which ignites his fascination with outer space and the tantalizing possibility of extraterrestrial life.
As the years pass, Elio develops a deep obsession with the idea of meeting aliens, often fantasizing about being abducted. He notes a disengagement with Olga, attributing it to her sacrifice of her dreams of becoming an astronaut for his upbringing. During one of his nightly excursions to the beach in hopes of contact, Elio encounters two boys, Bryce (portrayed by Young Dylan) and Caleb (played by Jake Getman). A clash ensues, culminating in Elio accidentally injuring himself with his ham radio, leading to his aunt picking him up from the hospital sporting a patch over his eye.
Frustrated, Olga takes Elio to work at her base, where they meet Gunther Melmac (played by Brendan Hunt), a scientist who believes they have received a message from another planet via the Voyager. Intrigued, Elio sneaks into the room and leaves a message expressing his desire to venture into space, but the message inadvertently triggers a blackout at the station. Angered by the incident, Olga resolves to send him to a summer camp, The Carver Academy. Feeling neglected, Elio argues that Olga is not family, deeply straining their relationship.
At camp, Elio discovers that his newfound friends, Bryce and Caleb, are present, while he continues his quest to communicate with aliens, causing friction with the bullies. Meanwhile, at Olga’s workplace, glitches arise on the computers as the message “Bring us your leader, please” flashes. As Elio tries to escape the bullies, a portal opens, pulling him into a realm of cosmic intrigue known as the Communiverse, where leaders from various planets converge to share knowledge.
Once inside, he encounters the liquid supercomputer, OOOOO, who assists Elio in connecting with extraterrestrial diplomats including Ambassador Questa, Ambassador Helix, and Ambassador Tegmen. They mistakenly believe he is the genuine leader of Earth. Yet, the peace is threatened by the tyrannical Lord Grigon, a menacing figure from the Hylurkian race, who seeks domination of the Communiverse. Faced with imminent danger, the ambassadors prefer to send Elio home, but he offers to confront Grigon directly to prove himself.
With guidance from OOOOO, Elio creates a clone dubbed "Other Elio" to maintain his presence on Earth. Upon arrival at Grigon's ship, Elio attempts diplomacy but fails, ending up imprisoned by Grigon. At the same time, Other Elio returns home, impressing Olga with his newfound sociability after receiving a more amicable persona from camp.
In the dungeons, Elio befriends Grigon’s kindhearted son, Glordon, who is imprisoned and reveals his innocent nature. Together, they hatch a plan to leverage Glordon as a bargaining chip against his father. They evade danger, with Elio hiding within Glordon's mouth to escape lava. Ultimately, they communicate with Grigon, and in a comical twist, Elio uses Glordon's innocence to negotiate peace, pulling off a ruse that leads to Grigon's reluctant agreement to back down.
However, the tension escalates as Grigon realizes he’s been duped when Elio’s clone fails to convince him. Enraged, he captures the ambassadors and wreaks havoc in search of Glordon. After chaos ensues, Elio is transported back to Earth, where he finds himself questioning his identity as Other Elio takes his place.
Facing adversities head-on, Elio joins forces with Olga to confront Grigon back at the military base after Glordon’s ship crash-lands on Earth. Following a touching reunion, they hastily prepare for a voyage to save the Communiverse. The ship's journey is perilous as it nears a debris belt, but through teamwork and camaraderie, they skillfully navigate to safety.
Upon reaching the Communiverse, Elio and Olga confront a desperate Grigon, who is utterly transformed seeing his son in danger. In a moment of clarity, he renounces his tyrannical ways, embracing Glordon’s wish to carve his own path. Elio is finally recognized as an ambassador himself, but he chooses to return home to be with Olga, leaving the door open for future adventures.
The story concludes with Elio and Olga witnessing their return to Earth, where both the camp and the military base rejoice at their arrival. In a playful end credit scene, Elio and Bryce reconnect using his ham radio to reach out to Glordon. The closing shot hints at further cosmic tales in the upcoming Pixar adventure, “Hoppers.”