Dr. Regal, a world authority on super energy, is invited to SciLab to study the Dimensional Converters. As soon as MegaMan and ProtoMan jacked into the Dimensional Converters repaired by Regal, the Dimensional Converters were activated and a Dimensional Area was generated. The energy source for the Dimensional Converters was the NetNavi SparkMan, who was ordered to destroy the Dimensional Converters, and he overwhelms C.F. MegaMan and C.F. ProtoMan before leaving. Regal regrets what happened, thinking it was due to his own experiment...

GravityMan is attacking the city. Lan and MegaMan struggles in their fight against him, but PrisMan and his NetOp, Misaki, come to the rescue. Misaki is actually the young man who failed in the Cross Fusion experiment, but now works for the NetPolice with a strong sense of justice. Meanwhile, SciLab has finish the development of the Battle Chip Gate, which can send unlimited chips to C.F. MegaMan, but something goes wrong. After receiving the intel, Lan and Misaki immediately arrive to the Dimensional Area where GravityMan is running amok, however... Misaki is overcome with his desire to CrossFuse, and Ms. Yuri uses his desires to lure him toward a trap. Meanwhile, Chaud assists Lan with the Battle Chip Gate to delete GravityMan using the Program Advance.

DenTech City is suffering a powerful heat wave! Luckily a new personal air conditioner arrives just in time to keep everyone cool. But a Grave general, a NetNavi called FreezeMan, uses their power to freeze DenTech City, and the weather flips from heat wave to blizzard! When his friends are turned to ice, Lan, convinced the cause of the freeze is in NetCity, plods through the frozen streets desperately searching for some place to jack in MegaMan But once in NetCity, MegaMan is overpowered by the fearsome FreezeMan! Just as MegaMan is on the verge of defeat, a mysterious new NetNavi, HeatMan, arrives to challenge FreezeMan. But who is HeatMan, anyway?

Revived, ShadeMan plans to get revenge on Dr. Regal. First, he captures Rush and uses his technology to appear in the real world without the aid of a Dimensional Area. He goes on a rampage through DenTech City to find Dr. Regal, but Lan intervenes. However, once Dr. Regal appears, he unveils a tower of Dimensional Area Converters and covers the entire planet.

All contact with NetNavis in DenTech City's moon station has been lost! While Commander Beef rockets to the moon to investigate, Lan and his friends are trying to learn more about the mysterious new "ExtraCodes" rumored to make NetNavis mightier than ever! Then Commander Beef encounters a dangerous new NetNavi, PlanetMan, who's trying to take over the moon. But before the Commander can react he's locked outside the lunar station with only two hours of air left! With Mr. Famous's help, Lan and his friends rush to the space center and beam MegaMan and GutsMan to the moon's cyber station to battle PlanetMan. But even with MegaMan now wielding an ExtraCode to get the amazing Aqua Custom Style, will he be able to handle its awesome, energy-draining power?

When Lan is hired to find out what is causing the city's lights to burn out and destroy themselves, Maylu discovers Lan is a NetSaver. Lan finds himself battling with Darkloid FlashMan only to be interrupted by Maylu, who wishes to help. MegaMan becomes damaged with Roll's clumsy battling style, and Dr. Hikari has to repair him. However, FlashMan strikes again, so Maylu rushes off to defeat FlashMan and amend her mistake. In the end, FlashMan is defeated when MegaMan and Roll fuse their souls together and create Roll Soul.