Gene is an emoji that lives in Textopolis, a digital city inside the phone of his user Alex. He is the son of two meh emojis named Mel and Mary, and is able to make multiple expressions despite his parents’ upbringing. His parents are hesitant of him going to work, but Gene insists so that he can feel useful. Upon receiving a text from his crush Addie, Alex decides to send her an emoji. When Gene is selected, he panics, makes a confusing expression, and wrecks the text center. Gene is called in by Smiler, a smiley emoji and leader of the text center, who concludes that Gene is a “malfunction” and therefore must be deleted. Gene is chased by bots, but is rescued by Hi-5, a once popular emoji who has since lost his fame due to lack of use. He tells Gene that he can be fixed if they find a hacker, and Hi-5 accompanies him so that he can reclaim his fame.
Smiler sends more bots to look for Gene when she finds out that he has left Textopolis, as his actions have caused Alex to think that his phone needs to be fixed. Gene and Hi-5 come to a piracy app where they meet the hacker emoji Jailbreak, who wants to reach Dropbox so that she can live in the cloud. The trio is attacked by Smiler’s bots, but manage to escape into the game Candy Crush. Jailbreak reveals that Gene can be fixed in the cloud, and the group goes off into the Just Dance app. While there, Jailbreak is revealed to be a princess emoji, named Linda, who fled home too after tiring of being stereotyped. They are once again attacked by bots, and their actions cause Alex to delete the Just Dance app. Gene and Jailbreak escape, but Hi-5 is taken along with the app and ends up in the trash.
Mel and Mary go searching for Gene and have a very lethargic argument. They make up in the Instagram app when Mel reveals that he, too, is a malfunction, explaining Gene’s behavior. While traveling through Spotify, Jailbreak admits that she likes Gene just the way he is, and that he should not be ashamed of his malfunction. They make it to the trash and rescue Hi-5, but are soon attacked by an upgraded bot. They evade it and enter Dropbox, where they encounter a firewall. The gang get past it with a password being Addie’s name and make it to the cloud, where Jailbreak prepares to reprogram Gene. Gene admits his feelings for Jailbreak, but she wishes to stick to her plan of venturing into the cloud, unintentionally causing Gene to revert to his apathetic programming out of heartbreak. The upgraded bot takes Gene, and Hi-5 and Jailbreak race after them.
As Smiler prepares to delete Gene, Mel and Mary arrive and are also threatened. Jailbreak and Hi-5 arrive and disable the bot, which falls on top of Smiler. Alex has since taken his phone to the store and asks to have his phone erased to fix the problem. Out of desperation, Gene prepares to have himself texted to Addie, making numerous faces to express himself. Realizing that Addie received a text from him, Alex stops his phone from getting erased, saving the emoji and finally getting to speak with Addie. Gene accepts himself for who he is and is celebrated by all of the emojis.
In a mid-credits scene, Smiler is seen wearing numerous braces due to her teeth being cracked by the bot, playing and losing a game of Go Fish in the “loser lounge” with the other forgotten and unused emotions, implying that she was demoted for her crimes.