The film takes place inside the world of a cellphone owned by a teenager named Alex (Jake T. Austin). In Textopolis (which is the texting part of Alex’s cellphone), emoji’s are sentient beings but have one purpose in life to match their representations. One emoji named Gene (T.J. Miller) is suppose to be a ‘meh’ emoji that shows indifference to just about everything, but he has trouble doing so as he is able to express more than one emoji, much to the concern of his father Mel (Steven Wright), but is supported by his mother Mary (Jennifer Coolidge). Mel plans to have Gene set his first day of work out, but Gene persists that he can make the right face, so his dad concedes.
On Gene’s first day of the job, Alex chooses him to send a text to a girl who he has a crush on, Addie Calister. However, Gene gets nervous and accidentally makes the incorrect face, making Alex decide to take his phone to the phone store to have it reset. Gene’s blunder causes the control-freak head Emoji, Smiler (Maya Rudolph) to label Gene a ‘malfunction’ and plots to have him deleted, but Gene manages to escape and is saved from Smiler’s robot henchmen, the Superbots, by an eccentric hand emoji named Hi-5 (James Corden), who was originally in the favorite’s section of Alex’s phone before being taken down. Hi-5 takes Gene to the ‘loser lounge’, a remote location where emoji’s who are hardly used hang out. After hearing some offhand talk about ‘hackers’ and how they can fix malfunctioning emoji’s, Gene sets off to find a hacker and have himself fixed to just being a ‘Meh’ emoji before Alex wipes the phone the next day. However, he must exit Textopolis, which is forbidden, to find one in Alex’s ‘piracy app’; to which Gene decides to do and Hi-5 tags along with him, hoping that Gene can get him back into the favorite section.
Smiler eventually finds out about Gene leaving Textopolis and sends her Superbots to go and find him before Alex has his phone wiped. Mel and Mary set out on their own quest to find Gene before Smiler’s robots do; but they repeatedly bicker and soon, Mel reveals that, like Gene, he too can make more than one emotion, but hid it from the other emoji’s. Gene and Hi-5, meanwhile, make it to the piracy app and find a hacker named Jailbreak (Anna Faris), who has her own agenda, to go to the iCloud on Alex’s phone and live there forever since nothing can get erased on it, but it is guarded by a firewall. Gene agrees to help her if she helps him become a permanent ‘meh’ emoji, to which she agrees. After a plethora of adventures between some apps, one of which has Jailbreak reveals that she was a princess emoji, but went rouge when she wanted to be more than that, Gene, Jailbreak, and Hi-5 make it to the firewall and Gene uses his multi-expressions to guess the password since only one emoji emotion can use it once. After numerous failures, which results in Gene getting completely burned, Hi-5 manages to help them when the firewall asks who Alex’s crush is as he saw the name during the adventure.
They make it to the Cloud, but Gene has second thoughts on wanting to be reprogrammed as a permanent ‘Meh’, as he has fallen in love with Jailbreak and has coe to appreciate her rebellious nature to what she was made for. He expresses his feelings to her, but she politely spurns him, wanting to be independent on the cloud. Heartbroken, Gene leaves the cloud to return to Textopolis, but is captured by one of Smiler’s Superbots and taken to the Textopolis theater where Smiler tries to have him deleted. Hi-5 witnesses gene’s capture and warns Jailbreak, who decides to abandon her mission and save Gene b yreverting to her original princess form. Gene’s parents come and Mel reveals his multi-expression malfunction, causing Smiler to decide to delete him to. However, Gene and his fatehr are saved by Hi-5 and Jailbreak, who, in a following confrontation with Smiler, is revealed to be Smiler’s daughter and that her real name is Linda.
Alex takes his phone to the shop to have it wiped and during the process, Jailbreak helps Gene make it to the emoji bar to convince Alex to change his mind. However, Addie arrives at the shop and reveals that she likes the emoji Alex sent her, which was Gene’s multi-expression face that he made when on the first day of his job. Amazed at this, Alex asks Addie to the dance, to which she accepts and Alex intercepts the phone wiping before it is complete, vowing to hold on to Gene as his favorite emoji. Gene is hailed a hero and receives a specially made emoji cube for him and Gene is happy that he can now express more than a single emotion.