Seasons & episodes

Zoano LarkMan is sent to help GateMan, and he turns his attention to Iris who has appeared on the ship with Lan. Meanwhile, Beast-MegaMan continues battling GateMan until the Zoanoroid is eventually deleted. As LarkMan prepares to defeat Lan and Iris, Chaud arrives on the scene and battles with the Zoanoroid using CrossFusion. Thus, everyone is saved, and Dr. Hikari and Maylu are returned from the depths of the ocean.

The NetSavers decide to capture the mysterious female NetNavi for information, and Trill is used as bait, but Zoano SnakeMan of Falzar and Zoano GutsMan of Gregar decide to try and capture Trill as well. MegaMan's friends battle with the Zoanoroids to protect Trill while Chaud tracks down Iris for answers. Iris and Trill descend from Beyondard, a world torn by the war between Gregar and Falzar, legendary cyber beasts. The key to restoring Beyondard lies within Trill, the "Synchronizer."

Zoano SnakeMan and Zoano GutsMan are subdued, but Zoano DarkMan is issued to capture Trill himself. The heroes are overwhelmed by his power, but Iris's NetNavi is able to assist in the protection of Trill, and she carefully houses him within Iris's PET. However, upon appearing in the real world with a CopyBot, DarkMan captures Iris and uses a device that opens a portal to Beyondard in the real world, and Lan, Chaud, Raika, Dingo, and Maylu are transported there with him.

Iris transports Trill away from her PET to somewhere in Beyondard where DarkMan cannot take him. Meanwhile, the children awaken in Beyondard, a world where both human and cyber worlds are one, and NetNavis and viruses can interact with humans directly. Maylu and Chaud reunite, as do Dingo and Raika, but Lan is left alone. He encounters Baryl and Colonel; they are Beyondard alternates of their original bodies and do not know Lan. When Zoano SnakeMan appears searching for Trill, MegaMan substantiates and defeats him.

Maylu and Chaud meet a train conductor named Al Ferry, operator of train-themed NetNavi ChargeMan. He lives in a village where the railroad network has prospered. However, Zoano JunkDataMan has been threatening the village by eating the tracks, and he sends viruses to cause more mischief. Chaud and Maylu offer to help, and ProtoMan substantiates to battle with JunkDataMan.

Lan travels to a fishing village where he meets a boy named Mick and rescues him from viruses. Mick takes Lan home to feast on a meal created by talented chef Pat Fahran. Pat has a dark past when a luxury liner she worked for was sunk by Zoano WhaleMan and she was the lone survivor. When Zoano WhaleMan appears to attack the village again, she seeks revenge with her NetNavi SlashMan. Lan also reunites with Trill.

Raika and Dingo meet an elderly man named Feng Tian who claims to know of Lan's location. However, his delinquent personality only causes trouble for the duo. Meanwhile, Beyondard alternates of Viddy and VideoMan harass the people of Amita, a village they have control over, so Raika and Dingo oppose them. Feng Tian also offers a hand with his own NetNavi, TenguMan. In the end, Raika and Dingo reunite with Lan.

While searching for Lan, Maylu and Chaud meet Moliarty and Press, NetOps of GroundMan and DustMan respectively. They're given a job by the Beyondard alternate of Ms. Millionaire to excavate through a rocky mountain for a precious item on the other side. Maylu and Chaud offer to help in the difficult excavation. (This is the only episode in the entire franchise where neither Lan nor MegaMan make an appearance.)

While searching for ingredients for Pat's curry, Dingo and Trill encounter DiveMan and follow him to a nearby lake castle. Inside, they discover that two humans, Captain Blackbeard and Yuika, are cooperating with Zoano DarkMan and have taken Iris prisoner. Dingo and Trill infiltrate the castle in hopes of rescuing Iris, but they must battle with Yuika's NetNavi, CircusMan. In the end, Iris is rescued.

Iris urges her friends to go to the Dimensional Area Laboratory, and they oblige. However, along the way, Zoano JapanMan appears and makes the journey difficult for the children, but their NetNavis substantiate and battle. Iris is damaged during battle, though, and revealed to be nothing more than a CopyBot. Reaching the lab, the children meet a holographic image of Tadashi, the Beyondard alternate of Lan's grandfather. He explains Beyondard's past before the children discover a war-torn Baryl outside of the lab.

An invasion is led by the Falzar army's Zoano CloudMan to destroy the Dimensional Area Laboratory. MegaMan, Roll, and TomahawkMan substantiate to fight back while Chaud and Raika operate the lab's defense system against the army. However, the great beast Falzar appears before the heroes, so MegaMan Beasts Out to retaliate. After the battle, the children are approached by an evil Colonel who threatens them, but Iris wards him off with her own energy.

On the way to the Wily Laboratory, Lan and his friends are attacked by Zoano CutMan, but a mysterious NetNavi EraseMan appears to delete CutMan himself. EraseMan is operated by the enigmatic boy named Dark Scythe who seems to have a connection to the Beyondard alternate of Maysa. Meanwhile, the younger brothers of CutMan formulate a plan to get revenge on Scythe by holding Maysa hostage.

Colonel has become a Zoanoroid and begins a rampage on the cities, and the children encounter him on their journey to the Wily Laboratory. Colonel attempts to capture Trill, but the children fight back. Meanwhile, Zoanoroids begin to invade DenTech City, and Dr. Hikari reassembles the CrossFusion Members to retaliate.

As Gregar and Falzar appear and begin battling, Blackbeard and Yuika (who are working for Beyondard Wily) succeed in capturing Trill. Falzar falls to Gregar, and Wily uses Trill as the synchronizer to combine both beasts into one. Creating the Super Cyber Beast Grezar and using it as his vessel, Wily begins to destroy both worlds.

The CrossFusion Members continue to deal with the Zoanoroid threat in DenTech City. Meanwhile, many Beyondard residents attempt to fight back against Wily but all fall short. In the end, in order to defeat Wily, Trill and MegaMan combine their powers and Lan performs Cross Fusion, merging into a new "Juuka Style." With this ultimate power, Lan is able to destroy Wily and close the portals between both worlds. With peace restored, Lan and his friends return home, but not before saying goodbye to new friends Trill and Iris.

Lan struggles with the memories of Beyondard, but everyone becomes well-adjusted to returning home. Peace isn't maintained for long, however, when strange cyber weeds appear all over a factory in Sharo, and Raika is forced to deal with substantiated viruses. The same thing soon occurs in DenTech City, and upon the defeat of the viruses, Lan faces a strange humanoid being with long blond hair.

As the NetSavers discuss the strange events, a man calling himself "Professor" announces his plans for world chaos before launching another attack with beastisized viruses. As Chaud uses CrossFusion to battle them, MegaMan jacks-in and encounters the humanoid being before known as Zero. MegaMan uses Beast Out to chase Zero away.

Lan and Chaud approach a power plant where more cyber plants and viruses have appeared, and they battle to delete them. However, Zero invades the Sci-Labs and escapes with a handful of valuable data. Lan learns from Yahoot that Professor was once a member of the WWW. Lan, Maylu, and Dex travel together to where Yahoot believes the Professor is hiding, but instead, they find a sushi factory.

While investigating the sushi factory, Lan and co. encounter many sushi chef robots, but the Professor uses them to try and ward off the intruders. However, they make their way to the depths of the sushi factory to discover that the Professor was indeed hiding down there and is planning to revive the Super Cyber Beast.

Professor sends a pack of viruses after Lan. Meanwhile, Chaud also appears in the factory to aid Lan, but Zero intervenes. Chaud battles with CrossFusion and fails, but Chaud's bond with his NetNavi sparks a change of heart in Zero. Refusing to be a pawn of Professor anymore, Zero departs to live his own life.

The Super Cyber Beast is revived prematurely, and in its incomplete form, it begins to rampage through NetCity. Professor escapes, so Lan and Chaud send MegaMan and ProtoMan into the internet to battle with the beast. Using Beast Out, MegaMan is able to destroy the new threat, temporarily ending Professor's reign of terror.

When a series of foul-mouthed dolls distributed by AyanoTech goes missing, Yai asks Lan to investigate. Blackbeard and Yuika of Beyondard have wandered into DenTech City and are planning a criminal attack with the dolls. Enlisting BubbleMan in their plan, they find an abandoned CopyBot factory.

Blackbeard and Yuika cooperate with BubbleMan to steal materials for building giant-sized CopyBots. Both DiveMan and CircusMan jack-in to the giant CopyBot at once, creating a giant-sized combination of both NetNavis. Lan uses CrossFusion to thwart them.

Blackbeard and Yuika press Mr. Wily of DenTech City for cooperation, but Dusk arrives to chase them away. They learn that Mr. Wily is knowledgeable of CrossFusion and desire SynchroChips, and they devise a plan to steal some. However, they unintentionally steal Reverse SynchroChips, and upon using them, vanish into the cyber world.