神秘彗星接近地球，令地球的网路世界起波澜，巨大病毒竟然实体化到处搞破坏，当仁不让的热斗和炎山再次派拍档领航员洛克人和布鲁士攻坚，虽轻描淡写地打败病毒，但却找出问题所在，原来来自神秘彗星的外星领航员迪奥要「审判」地球，地球危在旦夕，凶险的战斗即将展开…..

神秘彗星接近地球，引起连场网路大战，先由洛克人和布鲁斯力斗科鲁迪，随而带出外星领航员迪奥要审判地球的重大问题。热斗和炎山以「双向融合」的方式分别带同洛克人和布鲁斯进入彗星网路，并找到外星领航员迪奥。迪奥表明对「双向融合」感兴趣，并要以此为题来考验热斗……

迪奥开始考验人类，首先赐行星生命体给心术不正的驯兽师犬饲猛雄。生命体化身为网路领航员野兽人后，网路世界乱作一团，热斗和炎山马上出动，但亦未能压制野兽人，幸好这时热斗之父祐一郎完成「异次元空间发电机」，提升了洛克人和布鲁斯的战斗力。经一番战斗，两领航员合力打败野兽人，让人类过了首关「试练」。

行星生命体的威胁 迪奥开始考验人类，首先赐行星生命体给心术不正的驯兽师犬饲猛雄。生命体化身为网路领航员野兽人后，网路世界乱作一团，热斗和炎山马上出动，但亦未能压制野兽人，幸好这时热斗之父祐一郎完成「异次元空间发电机」，提升了洛克人和布鲁斯的战斗力。经一番战斗，两领航员合力打败野兽人，让人类过了首关「试练」。

近日发生一连串的奇特窃案，失物尽是威利博士的收藏品，热斗和炎山合力侦查下，发觉最可疑的是情圣查理，洛克人和布鲁斯更与此人的领航员螺旋桨人在网路中交起手来，几个回合过后，真正窃匪沙漠人终亮相，其操控者竟是电视台导演砂山登，一时间，局面变得更混乱，最后洛克人和布鲁斯虽全身而退，但看来砂山登仍会再临……

热斗认识了一位行径大懵的OL叶月唯，后发觉此女已成为迪奥代理人斯拉的目标。斯拉利用她对公司的怨气，以行星生命体化成「石头人」袭地球网路，热斗马上派洛克人应战，但石头人实太利害，洛克人的武器全数被变为石头，幸好洛克人情急智生，改变战略，终打败石头人，令一切回復正常。

洛克人和布鲁斯参加「领航员赛车」，唯云云车主中有一个心术不正的西古雷，其执令斯拉有机可乘，一场弘扬体育精神的赛事顿成为赛车的「杀戮战场」。西古雷的闪光人屡出矛招，令多部赛车出事退出，洛克人和布鲁斯唯有奋力还击，最后将闪光人击败。西古雷虽败阵，但百足之虫的性格驱使他投向新WWW…

亚美罗巴发生类似陨石坠地的神秘大爆炸事件，热斗和炎山一众往查究，发觉此陨石坑有时空偏差的现象，后又受大批已灭绝的病毒袭击，幸好危急间一自称「卡尼路」的神秘领航员出现，为洛克人和布鲁斯化解危难。事后，炎山获得「迪奥徽章」，并决定留在亚美罗巴继续查究神秘大爆炸之事，热斗则返回日本…

网路罪犯高斯连同其领航员磁铁人被判重刑，其女儿特斯拉马上以「新WWW」领袖之名宣称要反击，如是者，由热斗挂帅的网路警察马上镇守监禁高斯的网路看守所。未几，果见已归附新WWW的犬饲和砂山攻来，经一番大战，当热斗以为自己稳操胜券时，特拉斯才亮出皇牌，一举劫走高斯和磁铁人，大壮新WWW声威。

际遇未如理想的「影像作家」纳尔西.秀被斯拉利用，以行星生命体「影像人」的力量弄得全电算市一片粉红，热斗和直升机师查理分别派领航员洛克人和螺旋桨人查究，结果演变成网路大战，第一回合洛克人和螺旋桨人吃了小亏。影像人食髓知味，再次出动，但这次洛克人已激出斗志，和螺旋桨人「灵体共鸣」，成功打败影像人。

新WWW的成员犬饲猛雄有所行动，派其网路领航员野兽人将市内的汽车变成野兽，一时间，全市乱作一团。热斗与名人一同展开行动，起初处处受制于「野兽汽车」，幸机智的热斗想出以敌制敌的一招，方令洛克人顺利进入网路世界，再加上神秘网路领航员卡尼路现身相助，洛克人终打退野兽人，令世界回復正常。

石屎森林 新WWW的成员犬饲猛雄有所行动，派其网路领航员野兽人将市内的汽车变成野兽，一时间，全市乱作一团。热斗与名人一同展开行动，起初处处受制于「野兽汽车」，幸机智的热斗想出以敌制敌的一招，方令洛克人顺利进入网路世界，再加上神秘网路领航员卡尼路现身相助，洛克人终打退野兽人，令世界回復正常。

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.

落泊的程式研究员伊汪因为得不到上司赏识而走入邪道，以其超级压缩方法来掳走众多领航员，网路战警炎山和拉伍追查之下，从热斗之父处得到灵感，诱出伊汪，大战随即展开，经一番苦斗，炎山和拉伍的领航员布鲁斯和闪电人合力打败伊汪的冰人，并将伊汪绳之于法。

骇客马克和哈利两兄弟为怕罪证落入网路警察真边手中，遂借用行星生命体重力人的力量来谋害真边，令真边掉进了体重急增的迷雾中，热斗协助追寻根源，混乱间搞出一幕潜艇飞天事件，经一番战斗，洛克人在卡尼路协助下终打败重力人，令一切回復正常，马克和哈利兄弟也难逃法网……

骇客马克和哈利两兄弟为怕罪证落入网路警察真边手中，遂借用行星生命体重力人的力量来谋害真边，令真边掉进了体重急增的迷雾中，热斗协助追寻根源，混乱间搞出一幕潜艇飞天事件，经一番战斗，洛克人在卡尼路协助下终打败重力人，令一切回復正常，马克和哈利兄弟也难逃法网……

坏蛋土门凯的领航员烧夷弹人在逃避追捕时躲进了烟花工人六尺玉燃次的PET中，并展开了一段奇缘。在燃次的教化下，烧夷弹人戾气渐消，但土门凯不肯放过他，且令他回復行星生命体的可怕面貌，期间热斗和洛克人加入战围，经一番苦战，终于阻止了一场大灾难。土门凯被绳之于法，而烧夷弹人则重获新生，正式成为燃次的拍档。

新WWW总动员干扰通讯卫星，藉此令世界陷于混乱。行动期间其总裁特拉斯遇上情圣查理。查理不畏风暴将特拉斯送到「工作地点」，此举打动了特拉斯的心扉，但两人毕竟是对立者，当查理知道自己助纣为虐后，马上补过，派螺旋桨人修復被干扰的卫星系竟，化解了一场灾难。

干探岬悟郎昏迷三个月后甦醒，随之而来的是一场网路大战，军用的领航员卡尼路受重创，返送到科学省急救，接而来的是连串银行数据失黐市件，当中又涉及威利博士之女百合子。洛克人出动对付偷取银行数据的行星生命体炸弹人，经一番苦战，在稜镜人和针状人的配合下，终打败炸弹人，平息了一场风波，唯在背后搞事的特斯拉又有新目标….

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.

新WWW总裁特斯拉为自己预祝生日，派其手下每天都在网路中搞小动作，令网路战警热斗疲于奔命，幸好网路警探岬悟郎看出事件脉胳，出计替热斗锁定敌人踪迹，唯洛克人以寡敌众，全程均佔下风，幸最后关头百合子的领航员针状人出现，击败特斯拉的磁铁人，局面才扭转。

敌对的夏洛国和克里武兰国以合作研究「双向同步」而化解仇怨，分别代表两国的网路战警雷火和布莱特亦展开了友宜，但期间发生双向同步研究所遇袭事件，查看之下发觉已有一支行星生命体军团在冰城内蓄势待发，形势危急下，雷火和布莱特合力打败作梗的空气人，并消灭了军团，为两国建立了长久友好的基础

偷车贼阿剑派其行星生命体车灯人入侵汽车博物馆的展品「自动导航系统」，令市面的汽车成为他的囊中物，幸系统中的导述小姐露德通风报讯，让热斗和洛克人及时出战，经一番战斗，终打败车灯人，瓦解偷车集团之余，也保护了露德得尊严。

主题公园「恐龙天地」受不明病毒侵袭，热斗等人往查究，发觉乃新WWW成员纳尔西的杰作，随之而来的例牌是一场激烈网路对战。洛克人面对庞大的病毒军团和影像人，处处受制，危急关头，美露和领航员萝露借助拉修的晶片数据，成功进行「双向融合」，令洛克人得到足够的支援，反败为胜。

亚美罗巴的电脑网路出现可解开任何电脑锁的骇客，炎山和拉伍苦苦追寻下，终锁定犯人拉德，再追查下，又发觉教拉德开锁秘技的狱友将卡斯二十年前曾和神秘领航员卡尼路接触，疑云重重之下一场惨烈网路大战展开，最后炎山和拉伍的领航员布鲁斯和闪电人发挥威力，打败拉德。

新WWW总裁特拉斯因年龄问题而恼恨网路警察，趁网路警察搞机械人擂台赛时发烂，攻击力极强的机械人FP30顿成为她的俘虏。乱局一发不可收拾之际，热斗和烟花工人六尺玉燃次力战FP30，但特斯拉确实怨气太深，连融合后的洛克人也佔不到甜头，最后还是由特斯拉之父来解开困局…

早被删除的黑暗机器生命体阴影人透过过去隧道重生，来到现世，以强悍的战斗力力压洛克人和布鲁斯之余还令野兽人及闪光人吃尽苦头。热斗之父祐一郎想出「返回过去」之法来解决此事，遂安排洛克人和布鲁斯返回二十年前的世界，但这时阴影人出现，挟持洛克人和布鲁斯，齐齐进入了过去世界…

洛克人、布鲁斯和阴影人透过过去隧道进入了二十年前的网路世界，经一番战斗，神秘的卡尼路出现，协助洛克人对抗阴影人，但耐何洛克人竟染上黑气，一时间失去常性，幸卡尼路和布鲁斯仍然奋勇作战，为热斗制造出传送疫苗晶片的空间，洛克人接触过疫苗后醒觉过来，返回现实世界，但危机仍然存在….

丁戈发现自己的「图腾大人（图腾柱）」柱被安放于博物馆中，遂用尽一切方法盗取之，殊不知新WWW成员也视之为抢夺目标，双方交起手来，同时间，热斗得知新WWW有所行动，亦加入战围，一场混乱的网路战随即展开，经一番战斗，丁戈的领航员战斧人使出浑身解数，打败新WWW的领航员，除力保「图腾大人」不失外，还引证了自己的「迪奥选定者」身份。

乔伊娜少女茉莉花再次来到日本，热斗当然耐心地招呼她，期间发生海豚被虐事件，喜爱动物的茉莉花追查下发觉原来新WWW的成员犬饲利开海豚来贩运黑暗晶片，遂伙同热斗挑战恶势力，两人的领航员美蒂和洛克人力战野兽人，过程惊险万分，但邪不能胜正，野兽人最后也落得败走收场。透过此战，茉莉花亦确定了自己乃被迪奥选中的人。

市内举行「金冠小姐选举」，包括色绫丹居、特斯拉、真边等一众有自信的美女马上报名参加。比赛有结果，早想抢夺金冠的特斯拉使诈获胜，成为冠军，更马上在众目睽睽下展示盗黐本能，随即而来的当然是一场网路对战。特斯拉败阵，夺金冠好梦成空，后补而上的冠军是众望所归的玛莉老师。

萝露等领航员突然受袭，证据显示乃洛克人所为，令热斗一时间摸不头脑，经一番查究，发现原来乃洛克人的共同体「黑暗洛克人」的杰作，目的是要消灭洛克人。黑暗.雅和百合子救出被困的洛克人，造就一场洛克人对黑暗洛克人的决战，结果双方旗鼓相当，打成平手。事件过后，一切回復平静，但黑暗洛克人仍在暗角冷笑，准备捲土重来….

一向以拥有发亮额头而自豪的绫小路伊朵来日本搞「光额小姐选举大会」，并邀请烟花匠六尺玉燃次为她主理烟花演，期间黑洛克人的手下暴风雪人和乌云人来袭，热斗等人马上派领航员应战，经一番激战，暴风雪人和乌云人败走，伊朵的盛事顺利进行，而对于热斗来说，最大收获乃发觉六尺玉燃次亦是迪奥徽章拥有者。

近日时兴恋爱占卜，适值热斗又经常和茉莉花出双入对，一向心仪热斗的美露当然醋海翻波，情急下唯有求教于恋爱占卜大师安藤.朗美达，唯见朗美达竟然被行星生命体星星人害得惊惶失措，一心要盖过茉莉花的美露马上和萝露来一个「双向融合」，力战星星人，最后在热斗的支援下大获全胜。

新WWW一众向网路警察展开大反攻，先破坏异次元空间发电机，再选正日食时出击，令热斗无法和洛克人作「双向融合」应战，结果全电算市陷于一片混乱。这时，旧有的WWW组织看不过眼，决定和新WWW对干，弄来了已报废的异次元空间转换车，让热斗可和洛克人双向融合，一举击退敌人，力保电算市。

攻佔刚落成不久的轨道升降机「触天塔」，并以卫星坠地来唬吓世人，其时热斗和美露正处身触天塔内，正好和新WWW来个大对决，经一番战斗，一对活宝贝终于战胜邪恶，败阵的新WWW成员全数陷法网，但这时怪事再起，原来黑暗洛克人已接收新WWW的设施，并准备向世界发动可怕攻击….

丁戈、茉莉花和查理等拥有迪奥徽章的网路战士突然失踪，令热斗百思不得其解。此时，黑暗洛克人再派其旗下的黑暗机器生命体攻击地球，热斗单人匹马应战，只能节节败退，这时候查理等人以双向融合的姿态加入战围，才令热斗松一口气，但毕黑暗生命体有备而来，大战一触即发….

黑暗机器生命体开动巨大的开矿机冲向闹市，令世人陷于恐慌中，但热斗的同步晶片受损，未能出战，眼看兵凶战危之时，丁戈等人及时以「双向融合」来应战，团结就是力量，一举击溃黑暗机器生命体大军，助人类逃过一劫。黑暗机器生命体虽行动受创，但其背后的指挥者终现身，正是理格尔博士….

忍者黑暗.雅老是执于行刺热斗，但又发觉热斗运数奇佳，于是信心开始动摇。深层博士派行星生命体剑人打劫银行，连番得手后遇上追查到来的热斗，一场惨烈的网路对战随即展开。眼见热斗处于下风，危在旦夕时，黑暗.雅出手相助，让热斗有机会反败为胜。战后，两人开始建立同伴关系….

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.