Tomoro Tenma lives in a world where human thoughts and emotions, known as e-Pulse, power AI devices called Sapotama. But when Digimon begin materializing from Sapotama and feeding on e-Pulse, society begins to fracture. After Gekkomon appears from his device, Tomoro joins Glowing Dawn, a secret team investigating rogue Digimon and the dark truth of a system both fueled and corrupted by emotion.

人間の思考や感情から生まれる「e-パルス」は、AIサポートデバイス「サポタマ」のエネルギー源として活用されていた。目覚ましい発展を遂げるその陰で、恐るべき怪物が現れる。e-パルスを喰らって進化する生命体「デジモン」である。 　　天馬トモロウは、サポタマから突如現れたゲッコーモンとの出会いをきっかけに、非日常へと巻き込まれていく。 　　賞金稼ぎを生業とするチーム「ゴールデンドーン」の沢城キョウたちとの共同生活を送るなかで、トモロウは決意を新たにする。 　　人間とデジモンが描く新しい未来とは──

从人类的思想和感情诞生的「e-脉冲」，被作为AI辅助装置「辅助蛋」的能量源被运用。 　　在社会获得显著发展的背后，恐怖的怪物出现了。 　　吞食e-脉冲进化的生命体「数码兽」。

The Digital World is becoming so overpopulated that the super computer Yggdrasill who governs the Digital World can no longer handle it. Its solution is Project Ark: to wipe out most of inhabitants with the X Program. Yggdrasill chooses a very small percentage to be moved to a new Digital World and then proceeds to destroy the old one. Some Digimon who were not chosen survive anyway, and they move to the new world with a rare gift known as the X Antibody; this antibody changes their appearance and makes them more powerful, while at the same time making them immune to the X Program. No longer in control, Yggdrasill uses the Royal Knights to destroy these X-Digimon, who are outcasts in the new Digital World.

Time has passed since that summer adventure, and there are even more children with partner Digimon now. However, because of their unique nature, many children face the looming shadows of persecution and being targeted for military use. While Taichi and Yamato are working to rescue children, they are attacked by mysterious Digimon.

In 2012, after the events of Digimon Adventure: Last Evolution Kizuna, the early adulthood DigiDestined—Daisuke, Miyako, Iori, Takeru Takashi, Hikari, and Ken—must reconcile their new responsibilities with their Digimon partners. But Rui Owada, a mysterious young man, appears, claiming to be the first human to partner with a Digimon–Ukkomon. Could Rui really have been the first-ever DigiDestined?