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The world is at peace again but not for long. BubbleMan.EXE, who is frozen by Colonel.EXE's Ice Seed in the past suddenly thaws. When he wakes up he finds Trill.EXE, a baby NetNavi. Then there is a fight between PlantMan.EXE and SparkMan.EXE, who are supposed to be deleted but they claim to be Zoanoroids and are fighting for Gregar and Falzar, who oppose each other. They are looking for the Synchronizer which turns out to be Trill and fight over him. Meanwhile, the Cybeasts that they serve appear and fight each other in the Net. They repel SearchMan.EXE, ProtoMan.EXE and MegaMan.EXE's attempts to fight them. Then Trill runs into MegaMan and they Beast Out and become strong enough to repel them.
Now the Zoanoroids are invading Earth from Beyondard, en-masse and attempt may times to steal Trill. Half the series is spent in the regular world, protecting Trill and the other half is spent in Beyondard, searching for him. They find him and fight against the Cybeasts.
- Opening Theme: "Shouri no Uta" by Dandelion
- Ending Theme: "Ashiato" by Clair
List of episodes
- "Biyondādo" (ビヨンダード) Beyondard
- "Zoanoroido" (ゾアノロイド) Zoanoroid
- "Kopīroido" (コピーロイド) Copyroid
- "Onibi o Yobu Muteki" (鬼火を呼ぶ霧笛) The Foghorn that Calls the Phantom
- "Bōsō Disupurei" (暴走ディスプレイ) Rampaging Display
- "Nettonabi Kaisō Keigaku" (ネットナビ改造計画) NetNavi Remodeling Scheme
- "Rokkuman o Hokakuseyo!" (ロックマンを捕獲せよ!) Capture Rockman!
- "Midori no Hitomi no Tenkōsei" (みどりの瞳の転校生) Green-Eyed Transfer Student
- "Kōri no Kokoro" (氷の心) Icy Heart
- "Nerawareta Toriru" (狙われたトリル) Aiming for Trill
- "Kaitei Esuōesu" (海底SOS) Ocean Bottom SOS
- "Toriru no Himitsu" (トリルの秘密) Trill's Secret
- "Shinkuronaizā" (シンクロナイザー) Synchronize
- "Biyondādo Tsu" (ビヨンダード2) Beyondard 2
- "Tetsuro no Ōkoku" (鉄路の王国) The Railroad Kingdom
- "Riōri wa Aijō!" (料理は愛情!) Cooking is Love!
- "Fūten Rōshi" (風天老師) Futen Roshi
- "Kōtetsu no Iwa" (鋼鉄の岩) The Steel Rock
- "Mizūmi no Himitsu De A~ru" (湖の秘密であ〜る) The Secret of the Lake, De A~ru
- "Dimenshonaru Eria Kenkiujō" (ディメンショナルエリア研究所) Dimensional Area Laboratory
- "Fuaruzā Shiurai!" (ファルザー襲来!) Falzer Invasion
- "Shinigami to Yobareta Shōnen" (死神と呼ばれた少年) The Boy Called Death
- "Kāneru Bōsō" (カーネル暴走) Colonel's Rampage
- "Wairi Kenkiujō" (ワイリー研究所) Wily's Laboratory
- "Hikari o Koete" (光を超えて) Exceeding Light