The NetSavers are in investigation with the Sci-Lab over the strange comet that has appeared in Earth's atmosphere. Soon, strange activity begins occurring when giant-sized Mettaur viruses begin terrorizing DenTech City. Lan and Chaud manage to defeat them, but MegaMan finds himself captured by none-other-than Bass. He tells MegaMan that he is after his "Ultimate Program" so he can fight off Duo. As Lan and Chaud rush to his rescue, they encounter an old rival, Dr. Wily, who seems to know what's going on.

ProtoMan arrives to help ward off Bass, but more giant-sized viruses continue appearing in the real world. Lan and Chaud prepare to send their NetNavis to the comet, but Bass intervenes in hopes of overcoming the power that threatens Earth himself. Bass meets Slur who swiftly defeats him. Slur is a subordinate of Duo, an intergalactic force threatening to erase Earth after Dr. Regal's activity with darkness. However, Lan and Chaud convince him to spare their planet, and Duo challenges them to prove humankind's worth. After the incident, Lan receives a marking on the palm of his hand, the Crest of Duo.

BlazeQuest releases new PET models called Progress PETs. Meanwhile, while shooting a commercial for BlazeQuest, Lan meets Inukai, a zookeeper who is abusive to the animals. When Inukai gets in trouble, his frustration attracts Slur, and he is given Asteroid SavageMan to get revenge. Asteroid NetNavis are able to appear in the real world without Dimensional Areas, causing problems with Lan and Chaud, but Dr. Wily helps in the production of a Dimensional Area Generator, allowing the Sci-Labs to create them on command.

Mameo, a boy attending Lan's school, hates vegetables. Slur targets him and gives him Asteroid VineMan who can help destroy all of the vegetables in the world. This enrages Lan since vegetables are a prominent ingredient in curry, so Lan and Chaud track Mameo down. However, VineMan turns on Mameo, so Lan and Chaud must rescue him from his own NetNavi.

While investigating a NetSaver case, Lan notices helicopter pilot Charlie Airstar at the scene of the crimes. Lan presumes Charlie is the culprit, but Charlie is really tracking the true criminal on his own: director of DNN network, Sunayama (and even has the nerve of pursuing Sunayama to Lan's school). Sunayama uses Asteroid DesertMan to fight back, but MegaMan and ProtoMan team up with Charlie's GyroMan to stop him.

Clumsy Yui receives Asteroid StoneMan who gives her the power to turn anything she touches into stone. Panicking, Yui soon transforms the entire business complex and everyone inside into statues. Lan, who is returning an item Yui lost, encounters the problem and battles with StoneMan through Cross Fusion, as Yui had panicked and slotted the Dimensional Chip in.

Lan and Chaud represent BlazeQuest in a car race where NetNavis operate racecars in the real world and get into some comical arguments in the progress. Another participant, Rei Saiko, has mysteriously moved up in the tournament thanks to Rei's new NetNavi, Asteroid FlashMan, who has been cheating in the races. MegaMan and ProtoMan catch FlashMan in the act and are forced to battle with him by Cross Fusing, but Rei escapes before he can be arrested.

Lan and Chaud are led to Netopia to investigate a strange virus disturbance near a research center. There, strange holographic visions of the past appear, and viruses previously believed to be extinct attack in the real world. MegaMan and ProtoMan are also attacked, but they're rescued by a NetNavi named Colonel. After the incident, Chaud receives the Crest of Duo, and he decides to continue investigation in Netopia while Lan returns home.

Mr. Gauss's daughter Tesla announces the formation of a new net-crime syndicate called Neo WWW, and their first mission is to rescue the imprisoned Mr. Gauss. Lan and the NetSavers attempt to intervene, but with the aid of Inukai, Rei, and Sunayama who have all joined Tesla, Mr. Gauss is rescued and Tesla becomes the new operator of MagnetMan.

When film writer Viddy Narcy becomes enraged over the criticism of his latest work, Slur gives him Asteroid VideoMan. With VideoMan's help, Viddy begins painting the city in pink, including part of Lan's face. Lan teams up with Charlie to track Viddy down, and by forming GyroSoul with GyroMan, VideoMan is defeated. But as Viddy escapes, he encounters Sunayama who offers him a position in Neo WWW.

Inukai begins an attack by transforming automobiles throughout DenTech City into wild animals. Lan and Famous investigate the situation and MegaMan goes to battle with SavageMan but encounters all four Neo WWW NetNavis at once. Colonel reappears and rescues MegaMan in the end.

While visiting Dex in Jawaii, Lan meets Dingo, a fellow lover of curry. The two become quick rivals and Lan challenges him to a NetBattle with TomahawkMan. Meanwhile, Viddy plans to bury the entire island in a giant wave of curry sauce, so Lan and Dingo infiltrate his giant fish airship to stop him with some help from Dex, who Viddy kidnapped to make the curry sauce.

Lan meets a girl named Jasmine from the country of Choina. To complete her training as a pharmacist, Jasmine seeks a rare flower, and Lan agrees to help her. However, a man named Bengel in a medicine company hopes to steal the medicine that Jasmine is concocting, so he kidnaps Jasmine and threatens to delete her NetNavi Meddy if she doesn't give up her secrets. Lan and MegaMan manage to rescue the two from the perilous situation.

BubbleMan returns, and this time, he seeks a rare treasure hidden in the depths of the internet. He joins up with IceMan and SpoutMan to undergo this mission, but MegaMan and Roll are close behind to keep the young NetNavis out of trouble. MagnetMan also tails the group, hoping to snag the treasure for himself.

Chaud teams up with Raoul and ThunderMan to investigate missing NetNavis in Netopia. They track the crime down to Ivan Chilliski who was given Asteroid FridgeMan to undergo such crimes. Chaud and Raoul dupe him into revealing himself by posing as the afro-wig villains from Axess, and Chaud uses CrossFusion to battle with FridgeMan.

Mac and Harry, two criminals Manuela is pursuing, receive Asteroid GravityMan, and to get revenge on Manuela, they use him to shift gravity and make Manuela believe she is putting on weight. As a result, Manuela is overcome with the need to diet and exercise. However, Mac and Harry unintentionally appear in a submarine with the NetSavers during a virus examination, and they lose control of their NetNavi. Raika rejoins the cast at the end.

DarkChips have begun spreading through DenTech City again, so Lan begins an investigation in a factory to catch the culprits distributing the chips. He encounters Inukai and Rei who overcome him in battle. However, Raika reappears, now using CrossFusion to overcome the Neo WWW members.

Lan and Raika investigate the disappearance of ancient weapons being stolen from museums, and Raika suspects that his old friend Iriya may be operating Asteroid JapanMan who is responsible for the crimes. However, Iriya may be innocent when he tries to protect Raika from JapanMan. Lan and Raika delete JapanMan and bring Iriya back to his senses. Before returning home to Sharo, Raika receives the Crest of Duo.

Asteroid MoltanicMan was given to a criminal, but after an incident, a war-torn MoltanicMan drifts through the internet and finds himself in the PET of young fireworks-maker Fyrefox. Fyrefox is delighted to have a NetNavi after the loss of his own, and Fyrefox's friendship gradually sways MoltanicMan away from evil. However, MoltanicMan's original NetOp reappears, unwilling to give up his partner in crime to Fyrefox.

Lan and Dr. Hikari visit Taneka Island to help with the launch of a satellite. Meanwhile, Tesla is also visiting the island, planning to hijack the satellite. Before her attack, she encounters Charlie who quickly falls for her, and the two develop a flirtatious relationship. However, when Charlie discovers that the girl is really Tesla of Neo WWW, he rushes to the satellite to stop her attack.

Misaki finally awakens after the coma Dark ProtoMan put him into at Axess's conclusion, but he's discerned to learn that Ms. Yuri was never found. Meanwhile, Colonel faces Slur but is horribly damaged, so he's taken in to the Sci-Labs to recover. Before he can be questioned, he vanishes again. Back at the hospital, Asteroid BlasterMan attacks, and Misaki uses PrismMan to confront him. When cornered, Misaki is rescued than none-other-than Ms. Yuri who uses CrossFusion to defeat BlasterMan.

Dex has returned to DenTech City and, giving up his dreams of being the strongest NetBattler, has now embraced a life as a curry chef. Dingo also moves to DenTech to work for the original WWW's curry shop. Meanwhile, Sunayama and DesertMan work together in their latest scheme, but Yahoot, Dex, and Dingo work together to stop him.

Lan and Dex travel to Choina in hopes of finding a medicine for an ill panda bear in DenTech's zoo. There, they meet Cardamom, the grandfather of Jasmine. Meanwhile, many people in Choina wish to steal Cardamom's medicinal secrets, so Lan and Dex team up with Jasmine to help stop such a villain.

Yai holds a NetNavi design contest, and Viddy is so thrilled to participate that he quits his job with Neo WWW. However, upon winning the contest, Viddy is disqualified because the contest is restricted to children. Enraged, Viddy begins transforming AyanoTech's game characters into rabbits, but Lan and MegaMan intervene to stop Viddy's rampage. Viddy returns to his life at Neo WWW.

It's Tesla's birthday, and she desires more than anything her own SynchroChip. Through a series of crimes, the Neo WWW is able to retrieve her one, and she uses it to overcome Lan in battle. In the end, he is rescued by Ms. Yuri, but not before she has a special reunion with her twin sister Ms. Mari.

Sharo and Brightland cooperate in the production of a CrossFusion Research Institute, but Asteroid AirMan is sent to destroy it. Raika and Princess Pride work together to stop him, and they're chased to an abandoned castle amidst an ice storm where more secrets to this attack are unveiled. Raika ultimately defeats AirMan, and Pride receives her own Crest of Duo.

Lan meets Route, a guide program at an automobiles museum. Meanwhile, criminal Ken has to steal cars in order to rescue his girlfriend from a mob leader, and he is given Asteroid BrightMan to do so. Lan intervenes but is overpowered by BrightMan, so Route sacrifices herself in order to help defeat the Asteroid. However, Route is revived from back-up data, and peace is temporarily restored.

Lan becomes tired from constantly battling the Neo WWW, so Dex decides he wants to perform CrossFusion and help in the battle. He confronts Famous who uses Rush to create the Rush SynchroChip to help make it possible. Dex and Maylu accompany Lan to a dinosaur theme park where Viddy strikes, but Lan is too tired to battle. Dex attempts CrossFusion and fails, so in order to save the day, Maylu tries it. Surprisingly, she CrossFuses flawlessly and helps Lan defeat Viddy.

An investigation by Chaud in Netopia against a man named Rat leads to some shocking discoveries. A man named Jackass used the same crime tactics that Rat did, but his attacks were decades in the past, and Colonel was responsible for stopping him. Considering Colonel still exists in the present time, Chaud contemplates the true nature of his character. Chaud and Raoul ultimately capture Rat and defeat his Asteroid DrillMan, but not before his plan was put into motion, causing locks all over the world to suddenly unlock.

When a newspaper prints Tesla's age as thirty, she becomes enraged. During a robot battle convention, she hijacks a robot named Thirty and attacks the NetPolice. After a malfunction, the robot goes speeding after Lan and Fyrefox through DenTech City. Lan CrossFuses to battle with Tesla while Fyrefox sends MoltanicMan inside Thirty to prevent it from self-destructing.

Through Chaud's research, he knows more information regarding Colonel and his NetOp Baryl.[1] Meanwhile, a shift in time and space revives ShadeMan moments before LaserMan deleted him in Axess. He fights with Lan and Chaud, and Ms. Yuri helps, revealing that she, too, has a Crest of Duo. ShadeMan reunites with BubbleMan and begins their latest scheme to travel twenty years into the past, before the network was created, and overrun the world with Darkloids. MegaMan attempts to stop him but fails, receiving a painful bite on the neck as he falls.

MegaMan dives into the space-time tunnel and follows ShadeMan twenty years into the past. There, he encounters Colonel and teams up with him to save the future. However, the bite left by ShadeMan on MegaMan's neck infuses him with evil energy, transforming his soul into darkness. Lan rushes to connect with MegaMan again, hoping to install a VaccineChip and recover him. He does so just as ShadeMan is deleted, and MegaMan manages to stop his plan, returning the present time back to normal. As MegaMan returns to his time, the dark energy separates from his body and vanishes.

Shanka, a girl from Dingo's tribe, requests to return a stolen totem pole back to her village when it's discovered in a museum. However, Viddy and Inukai steal the totem pole along with other rare items, so Lan, Dingo, and Shanka work together to recover the ancient relics. In the end, Dingo receives the Crest of Duo.

Jasmine returns to DenTech City to take care of an injured dolphin named Hoshi (meaning "star"). Hoshi was injured when being used by the Neo WWW to smuggle DarkChips. Lan, Yahoot, Dex, and Jasmine team up to defeat Inukai and SavageMan in their latest schemes. In the end, Jasmine receives the Crest of Duo.

At a convention center, a Ms. Tiara contest is held with a chance for girls to win a golden tiara, and many girls from DenTech City enter. A rivalry quickly builds between Maddy and Tesla. Tesla attempts to steal the tiara, so Charlie appears to intervene, and all of the girls aid Lan in Neo WWW's defeat. Ms. Mari ultimately wins the contest, and both Charlie and Tesla receive Crests of Duo.

MegaMan has startling dreams where he murders his NetNavi friends, and he becomes nervous when he learns his friends were injured the night before. Though MegaMan's system tests normal, MegaMan begins causing mischief, leading to his eventual arrest. After an emotional separation, Lan realizes that he isn't MegaMan, and the NetNavi unveils himself as Dark MegaMan. The real MegaMan has been captured by Darkloids CosmoMan, LarkMan, BlizzardMan, and CloudMan. Ms. Yuri helps Lan rescue his NetNavi, and ShadowMan even reappears to assist. The Darkloids thus escape.

Dr. Hikari researches the Crests of Duo and discovers that those marked with it have higher synchro-ratings, meaning CrossFusion is more possible with them. Meanwhile, Yai is planning a fireworks party, so she urges Lan to bring Fyrefox and Mr. Match to help with the festivities. However, BlizzardMan and CloudMan attack with orders to delete MegaMan, and they transform the hall into a raging blizzard. Lan, Dex, Mr. Match, Dingo, and Fyrefox all team up to overcome the Darkloids, and Fyrefox is able to delete BlizzardMan in the real world using a firework dispenser. Fyrefox thus receives the Crest of Duo.

Lan introduces Maylu to Jasmine, but she quickly becomes jealous of the relationship the two have developed. Having been marked by Duo, Lan and Jasmine can see Duo's comet, but Maylu cannot. Likewise, Meddy and Roll compete for MegaMan's affection. Meanwhile, a fortune-teller named Romeda wants to make a huge prediction, so her NetNavi Asteroid NovaMan causes a meteor to come crashing down towards Earth. Maylu intervenes and helps Lan defeat NovaMan and stop the meteor. Together, they stand and watch Duo's comet, signifying Maylu too received the Crest of Duo.

Neo WWW calculate a plan to prevent the creation of Dimensional Areas. SavageMan destroys the Sci-Labs's Dimensional Generator, but the attack deletes SavageMan and hospitalizes Famous. Then, because of a solar eclipse, receiving Dimensional Area signals from across seas is impossible, and Neo WWW begins their attack with Lan unable to CrossFuse. The original WWW teams up with their old leader, Dr. Wily, to devise a plan against the Neo WWW. They prove victorious, and VideoMan is also deleted.

Lan and Maylu visit an orbital elevator that reaches into space. Once there, however, they become entangled in Tesla's next plan as she hijacks the elevator. Lan and Maylu use CrossFusion to battle DesertMan and FlashMan, succeeding in the deletion of both. As the final Neo WWW members are arrested, Tesla suddenly vanishes, and her four subordinates' memories are erased. Dark MegaMan has taken Tesla hostage in her own hideout.

Dark MegaMan's Darkloids invade NetCity and then retaliate against Lan in the real world, destroying his SynchroChip. To have it repaired, Lan travels to Sharo's CrossFusion Research Institute where Dr. Hikari is stationed. Along the way, the Darkloids attack again, but Lan is rescued by Raika and Charlie, and he is surprised to discover that Charlie has now CrossFused as well.

The Darkloids take over a large excavation machine and begin rampaging through Sharo. In order to stop them, the CrossFusion Members join together, including Raika, Charlie, Dingo, Jasmine, Princess Pride, and Fyrefox. While they battle, Lan's SynchroChip is stolen by Dusk, ShadowMan's NetOp. Ms. Yuri and SpikeMan intervene and Lan recovers the chip, but as Dusk escapes, he receives the Crest of Duo. The Darkloids escape, and it's revealed that Dr. Regal is commanding the Darkloids.

Dusk is an assassin commanded to delete MegaMan, but he hesitates for the Crest of Duo marks him as Lan's ally. Meanwhile, a bank robber similar to Dusk named Kawase uses Asteroid SwordMan in his crimes, so Lan and Dingo intervene. Dr. Wily offers Dusk the opportunity to live his own life outside of hired assassin work by giving him a SynchroChip, and with it, Dusk CrossFuses and rescues the boys.

Dr. Hikari and Famous bring the CrossFusion Members together at the beach for special training, but the training session is really just a relaxing vacation in the sun to help calm their nerves. Yai and Anetta also attend, as well as the original WWW members. The gang ends up exploring a haunted house, and Maylu continues to fight Jasmine for Lan's affection.

The CrossFusion Members meet with Chaud to explore ancient ruins discovered in Netopia which bare Duo's symbol. Inside, a holographic image tells of an alien race that travels to planets via Duo's comet and destroys civilizations that are deemed dangerous. Slur becomes enraged that the heroes have discovered the past of her race and commands the destruction of the ruins. The children barely manage to escape in time.

The CrossFusion Members formulate a plan to infiltrate Neo WWW's hideout and rescue Tesla. Also, the member's Crests of Duo have mysteriously faded away, the first three victims being Chaud, Raika, and Princes Pride. Count Zap also assists Mr. Gauss in the rescue of his niece. To pass security, the members must scan their hands. But once inside, the Darkloids Cloudman and LarkMan attack. Battling up to the top, they reach Dark MegaMan, who reveals that Mr. Gauss tricked the members into the tower in exchange for Tesla. The hand scans gave Dark MegaMan the data that rested within Duo's Crests. As the members escape the tower, Tesla CrossFuses and vanishes.

Charlie is startled to discover Tesla has been sleeping in his apartment. Meanwhile, Dark MegaMan lures Ms. Yuri into a trap to steal her Crest of Duo. When she refuses to comply, Dr. Regal then appears and steals it himself. Lan, Charlie, and Tesla battle with the remaining Darkloids, deleting CosmoMan and forcing Dark MegaMan to retreat. Dr. Wily explains that Dr. Regal needs the data within the Crests of Duo to achieve access to the power within Duo's comet. Dr. Regal has planned such a thing for decades as he had already taken Baryl's Crest twenty years ago when Baryl was alive.

The Asteroids begin invading Earth, and the CrossFusion Members fight to ward them off. However, until Slur is defeated, the numbers will only grow, so while the members battle the Asteroid invasion, MegaMan, ProtoMan, SearchMan, and Colonel jack-in to take Slur down themselves. However, their efforts are futile, and Slur easily overcomes them on her own.

Thirty years ago, Duo's comet had crashed on Earth, and Dr. Regal plans to travel through space and time to absorb its power. MegaMan, ProtoMan, SearchMan, and Colonel rush through time to thwart Dark MegaMan who was sent to help Dr. Regal gain access to the comet. However, Dark MegaMan plans to absorb the power himself and become the ultimate NetNavi, but Slur refuses to allow him to do so by deleting him. Before fading away, Dark MegaMan self-destructs and prevents Dr. Regal from succeeding. The heroes return home, and the renmants of Dark MegaMan's being rejoin with MegaMan's soul, and MegaMan forgives him.

Duo begins to erase the Earth, and in order to stop him, all thirteen CrossFusion Members must join together. However, Baryl has already died. Dr. Wily of the past works with Dr. Wily of the future to send Baryl through time and space using the Spectrum program. Once Baryl arrives in Lan's time, he receives a SynchroChip and uses CrossFusion to help his allies take down another invasion of Asteroids.

Bass reappears and now infused with the power of Nebula Grey, he deletes Slur. Meanwhile, Dr. Regal gains access to Duo's power and begins his attack on Earth, but Duo kills him before beginning the erasure of Earth. The CrossFusion Members travel to Duo's comet, avoiding demise as the Earth vanishes. They confront Duo, begging him to reverse the erasure, but Duo cannot comprehend their pleas, having more interest in CrossFusion instead, a technology similar to his own race's.

BubbleMan, who was frozen in cyber space by Colonel, finds himself freed when a strange energy appears before him. Left behind is an infant NetNavi. He carries it to NetCity before collapsing and being found by Roll and the others. Meanwhile, strange disturbances appear in the real world as two gigantic cloaked beasts begin battling. Lan, Chaud, and Raika intervene, and the beasts move their battle to the internet. When MegaMan battles with them, the infant's power combines with his own, and MegaMan defeats the beasts using two new styles modeled after the beasts.

Two NetNavis known as Zoanoroids are at war on the internet, one praising the lion Gregar (Zoano VineMan) and the other worshipping falcon Falzar (Zoano SparkMan). The Zoanoroids claim to descend from a world called "Beyondard." As they battle, MegaMan and ProtoMan intervene. Meanwhile, Roll takes care of the infant NetNavi who MegaMan decides to name "Trill."

Famous assists Makoto in the production of CopyBots (known as "Copyroids" in Japanese), robots that allow NetNavis to interact in the real world. However, once completed, Zoano Punk appears and forces Makoto to build more CopyBots for his army. Lan and Chaud learn of this and assist Famous in Makoto's rescue, but not before a truck-load of CopyBots are delivered to the Falzar army. Meanwhile Trill "grows" and acquires the ability to speak after a long sleep.

The NetSavers receive word of a phantom battleship, so Lan investigates. The ship is being controlled by Zoano FlameMan who plans to use it to destroy a warehouse on an island where Falzar's CopyBots are being held. MegaMan battles with FlameMan, but Trill, who is insistent on showing MegaMan that he is not afraid of ghosts, gets in the way.

Yai has moved back to DenTech City, and as a treat to her friends, she takes them to a holographic animal exhibit that's still under construction. However, the exhibit malfunctions and the children are chased by deformed zoo animals. The NetNavis are jacked in to stop the mess, but a crack in space is revealed, bringing prehistoric beast viruses from the world of Beyondard to threaten the heroes.

Chaud travels to Netopia to explore a military factory where BubbleMan was imprisoned by Colonel. There, he meets a mysterious young girl. Meanwhile, Zoano PharaohMan is capturing NetNavis and transforming them into followers of Gregar, including Zoano SparkMan. MegaMan intervenes and transforms with Trill into the Gregar Style to defeat the Zoanoroids, but as a result, loses control of his body and escapes into NetCity.

Lan's friends work together to try and subdue Gregar MegaMan who is rampaging through NetCity. Meanwhile, the mysterious girl appears before Lan asking of Trill before vanishing again. Later, a strange light forms over MegaMan, separating him from Trill before Trill also vanishes. A strange NetNavi attempts to return Trill to Beyondard, but he refuses, and ProtoMan appears to rescue the two from Zoano PharaohMan. ProtoMan takes Trill back to MegaMan.

The mysterious girl becomes a student in Lan's class, her name being Iris. Meanwhile, Zoano NumberMan appears and poses as Higsby's NumberMan in order to join his friends in visiting MegaMan (who is still recovering from last episode's damages). When the real NumberMan arrives, the two begin to battle until the true NumberMan is revealed, and the impostor escapes.

While playing in NetCity, IceMan encounters a fallen Zoanoroid FreezeMan, injured from a battle against Zoano StoneMan. FreezeMan was attempting to build a communication device for Falzar, and IceMan agrees to help retrieve it. When he returns, he finds FreezeMan in battle with StoneMan and attempts to protect his new friend, but FreezeMan sacrifices his own life to protect IceMan's. Both Zoanoroids fall, and IceMan builds a memorial grave for his deceased friend.

Lan and Maylu visit Dr. Hikari who is performing a deep-sea investigation. Zoano GateMan of Falzar and Zoano QuickMan of Gregar appear, both seeking to capture Trill. QuickMan battles with MegaMan while GateMan traps Dr. Hikari and Maylu underwater, threatening their lives if Trill isn't given up. QuickMan is defeated, but GateMan captures Trill and Lan's friends are not spared. MegaMan and Trill merge once more, and Beast-MegaMan assaults GateMan.

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.