Everyone in the world uses smartphone apps. But inside them lurks unknown creatures called "Appli Monsters," or "Appmon." The Appmon are AI lifeforms with the ability to think and act, and exist in the boundary between the human world and digital space. In the vast sea of the internet, the "last boss AI" Leviathan takes control of the Appmon with a virus and begins hacking every system, thus starting to control the human world from the world of the net. Haru Shinkai is led to acquire the Appli Drive, and uses it to materialize Gatchmon, a search app monster.
Eri, Torajirou and Rei bring their Appmon to the God Grade to confront Deusmon, while Haru is attacked by Yūjin. Still disheartened with the revelation that Yūjin is an enemy, Haru refuses to fight back, until Gatchmon succeeds in cheering him up.
Haru, Eri, Torajiro and Yūjin are invited to visit L Town, a city fully designed and operated by L Corp, where they encounter Cloud, a human who warns them to stop meddling with Leviathan's plans.
Torajirou is dragged by his uncle to a secluded temple for training and his friends set out to break him out. On their way, Rei warns Haru be careful arround Yūjin, as he is suspicious of him.
To stop Leviathan from taking over the world, the AppliDrivers must find Hajime's creation, the Appmon Bootmon before he is captured by the enemy, but during their search for him, another troublesome Appmon named Damedamon appears in their way.
Haru and the others set to rescue Yūjin and Offmon from the Ultimate 4, but are informed that they only have 60 minutes left before the two are killed. To proceed further, they must also confront some of their fallen enemies who were revived to fight them again.
MariPerorimon, the Appmon of a Gourmet App specialized on Mega Servings, look for Eri's help to increase her reviewing skills, but with Eri too busy with work, Dokamon offers himself to train her instead.
A summary of the events in the series so far.
Mienumon sends the Copy and Paste Appmon, Copypamon to cause a ruckus and torment Eri just when she is about to launch her first single.
Chasing after Rei in order to rescue the Seven Code Appmon he stole from them, Haru and his friends come across Sakusimon, another of Leviathan's agents, but are rescued by Rei, and learn the reason why he is gathering the Seven Codes for himself.
After losing control and injuring Yūjin in the last fight, Offmon decides to leave his side, but Satellamon appears to challenge Offmon again and Yūjin convinces him to trust their bond and fight the enemy together with Haru and Globemon's help.
Fed up with the others doting Offmon, Gatchmon runs away from home, and both Dokamon and Musimon decide to follow him. However, they meet a boy who is lost after also running away and the trio works together to help him find his way back to his family.
After gaining a new ally that can fuse with Gatchmon into the more powerful DoGatchmon and driving away Cameramon, an agent of the evil artificial intelligence "Leviathan", Haru pursues an Appmon that intends to transform the city's systems into a Role Playing Game.
AppliYama 470's general election is underway. Eri works hard to secure a position among the most voted idols, but in the last minute, a rogue Appmon out of devotion for her decides to mess up with the results, forcing her and her friends to intervene.
Haru and the others attend a meeting intending to meet the other Seven Code Appmon, but instead they are lured into an ambush by Hackmon and his Appli Driver Rei, who challenge them for a fight.
Haru meets Torajirou Asuka, a famous Apptuber who also happens to be an Appli Driver like him and Eri. Aside from his energetic demeanor, Torajirou also hides a strict side that is revealed when he and Haru confront an Appmon that is making watches around the world out of sync.
Haru's friends get themselves in trouble when their search apps go hawyire, and realizing that an Appmon is the culprit, he and Gatchmon confront it.
Upon learning that Bootmon is hiding at Haru's school, the gang devises a plan to finally catch him. However, when Bootmon is cornered, Yūjin reveals his true self and captures him under Leviathan's orders.
Eri earns a trip to a resort hotel and invites Haru and the others for it. However, they are misdirected by Tripmon, an Appmon serving under Satellamon, who is eager to take back at Offmon for stopping him in their previous encounter.
Haru, Torajirou and Eri are invited by their Appmon to participate in a competition between them, but the climax of the festivities are interrupted when a hostile Appmon called Hackmon arrives to challenge them.
Haru introduces Torajirou and Eri, but they soon start bickering due to their incompatible egos. Soon after, Torajirou becomes distressed upon learning of another Apptuber becoming far more famous than him, and his videos plummeting in popularity suddenly, unaware that an infected Appmon is involved.
Eri meets the gourmet Appmon, Perorimon, and attempts to appease him in order to bolster her career, but the plan backfires and Perorimon flees. Soon after, data from sites everywhere starts going missing, and both Eri and Haru start searching for Perorimon, wondering if he is involved, until they find the real culprit.
Mienumon decides to send Coachmon in another ploy to torment Eri. However, moved by Eri true desire to improve herself, no matter what harsh training he imposes, Coachmon reforms and helps Dokamon to reach the ultimate level.
Haru and co. join forces to help Rei storm the headquarters of L Corp in search for his brother, Hajime. But it not takes long for them to be discovered and they must fight their way against an army of Sleepmon to rescue him.
Rei steals some critical data while looking for Hajime, while the CEO of L Corporation is replaced by Knight Unryūji, a young boy working for Leviathan.
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