Gene is an emoji that lives in Textopolis, a digital city inside the smartphone of a middle school student, Alex. He is the son of two meh emojis named Mel and Mary and, unlike other emojis, he is able to make multiple expressions, which is frowned upon. His parents are hesitant about him going to work, but Gene insists so that he can feel useful. Upon receiving a text from his love interest Addie McCallister, Alex decides to send her an emoji. Gene is selected, who unintentionally makes a panicked expression and wrecks the text center. He 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. Hi-5 tells him that he can be fixed if they find a hacker, so the two go on an adventure; Gene to become a “normal” emoji, and Hi-5 to regain his popularity.

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 a hacker emoji named 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 who fled home 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 their son and have a very lethargic argument. They reconcile in the Instagram app when Mel reveals that he is also a malfunction, explaining Gene’s behavior. While traveling through Spotify, Jailbreak admits that she likes Gene the way he is and says he should not be ashamed of his malfunction. The two start to fall in love and Gene debates his choice to change himself. They make it to the trash and rescue Hi-5, but are soon attacked by a bot upgraded with illegal malware. They evade it by entangling its arms and enter Dropbox, where they encounter a firewall. After many attempts, the gang gets 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. Suddenly, the upgraded bot sneaks into the cloud and captures Gene, prompting Hi-5 and Jailbreak to go after him with a Twitter bird summoned by Jailbreak in her princess form.

As Smiler prepares to delete Gene, Mel and Mary arrive. Mel reveals to everyone that he is also a malfunction, prompting Smiler to threaten to delete him as well. Jailbreak and Hi-5 arrive and disable the bot, which falls on top of Smiler. Alex has since taken his phone to a store in hopes that a factory reset performed by technical support would restore his phone’s functionality, which would entail total destruction of Gene’s world should such operation complete. 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 cancels the factory reset just as it nearly finishes, saving the emojis and finally getting to speak with Addie, who likes the emoji Alex sent. Gene accepts himself for who he is and is celebrated by all of the emojis.

In a mid-credits scene, Smiler has been relegated to the “loser lounge” with the other unused and forgotten emojis for her crimes, wearing numerous braces due to her teeth being chipped by the bot, and playing and losing a game of Go Fish.