Manga
The manga consisted of six storylines, each loosely adapted the elements from the games. The first storyline follows Lan and MegaMan fighting against World Three in a villain of the week format. After a series of attacks by World Three, Lan and MegaMan developed a rare ability of Full-Synchro—a state where the operator and Navi's minds merge together allowing for quicker reactions at the cost of any damage on the Navi also being inflicted on the operator. Due to this, he is given a Net-Battler license and officially employed by the police to help in defeating World Three. Eventually, the leader of World Three, Dr. Willy, starts a massive attack on the world's electronics and intends to use his creation, the Life Virus, to control the satellites in space to destroy the Earth. Lan and MegaMan managed to find an opening and defeat the Life Virus with MegaMan got blown all the way to the underground internet, the Undernet.
In the second storyline, Lan and MegaMan fight the remnants of World Three, only to be suddenly attacked by the strongest Navi of the Undernet, the "Black Shadow" Bass. They are swiftly defeated, but promise each other to improve their skills for an eventual rematch. Both soon enter an ancient pyramid and encounter PharaohMan, a NetNavi coming from an ancient civilization who bestows them the power of Hub-Style upon his deletion. MegaMan's new power attracted the attention of criminal organization, Grave, who aims to rob MegaMan's power by using their Multibug Organism, Grave Beast. Bass joined the fight and started their long awaited rematch, with MegaMan emerged victorious.
After Grave's destruction, Lan and MegaMan were approached by a famous Net-battler instructor, Mr. Famous, who warned them of new enemies in the form of dark power led by the Quartet of Evil that rendered Hub Style useless. The dark power soon surrounds the city, causing Net Navis within to materialize in the real world. Mr. Famous assembled experienced Net-Battlers to combat the threat, but all were defeated save for Lan and MegaMan, and their friends, Chaud Blaze and ProtoMan who gained new power called the Muramasa-style from the King of Undernet, Serenade. Together, they defeat the Quartet of Evil, who have accumulated the darkness to revive Bass as a Dark Navi. Bass began his attack on the human world, absorbing Serenade in the process. Using the new program left behind by Serenade, Double Soul, MegaMan gained a new form, the Proto Soul, by absorbing 99% of ProtoMan's power and defeated Bass. However, after Bass' defeat, two Dark Navis, LaserMan and MegaMan DS (Dark Soul), revealed themselves as Darkloids, the true preparators of the Dark Navis.
The dark dome recedes and NetNavis return to their PETs and the Cybernet. With the assistance of a Net Navi from Schaero, SearchMan, and BubbleMan, they find the black hole that the Darkloids used to enter their world. MegaMan and Lan used Hub Style to entered the black hole and confronted by MegaMan DS who has ShadeMan separate MegaMan and Lan's consciousness, and severely injured Lan to make MegaMan gave in to his hatred, which reinforced MegaMan DS' power and allowed him to completely absorb Bass. ProtoMan and SearchMan followed MegaMan, and with their combined efforts as well as Bass rebelling from inside MegaMan DS, finally defeated MegaMan DS and LaserMan. A Netopia army led by NetNavi Colonel arrived shortly and destroyed the remaining the Dark Loids and close the portal to the Dark Cybernet. Days later, the Netopia army received the order to imprison MegaMan fearing a potential Double-Soul between him and Bass would result in world destruction, forcing MegaMan to be on the run.
Lan followed MegaMan to Netopia with Chaud's help and discovered that the Netopia Army has been infiltrated by the Darkloids. After proving himself trustworthy, Colonel and his operator Baryl allowed MegaMan and Lan to join their cause to defeat the Darkloids led by Regal. In retaliation, Regal unleashes the dark program Nebula Gray which threatens to absorb the Cybernet. The Netopia Military attempts to invade Regal's server but are wiped out by Nebula Gray except Colonel. Attracted by Nebula Gray's dark power, Bass also joined the fight, soon followed by MegaMan, ProtoMan, TomahawkMan, and GyroMan. Everyone but MegaMan, Bass, and Colonel were defeated, so MegaMan was left with no choice but to merge himself with Bass, becoming Bass Cross MegaMan. While they overpowered Nebula Gray, the dark program recovered itself by absorbing Bass' power. MegaMan found a new power called Beast Out and used it to finally deleted Nebula Gray.
Sometimes after the battle against Nebula Gray, MegaMan was approached by a NetNavi named Iris. She gathered potentially strong NetNavis and told them to fight against each other and the winner will be bestowed the ultimate program that capable of resealing Cybeast Gregar, the origin of MegaMan's Beast Out power. As the NetNavis battle each other to retrieve the loser's Navi Mark, another Cybeast called Falzar appeared and targeted him. MegaMan was given the Navi Marks of his friends, but was still incapable of defeating Falzar. Bass appeared and absorbed Falzar's power, but Gregar and Falzar fused with each other into Cybeast Grezar to replace the power they have lost. Their fusion turns reality into data and absorbs it, with only MegaMan and Bass left to fight Grezar. Eventually, MegaMan with his Super Beast Out power destroyed the Grezar's core and was seemingly deleted in the explosion, leaving Lan distraught. A year later, the Cybernet was re-opened and MegaMan returned, happily reuniting with Lan.
Anime
EXE is roughly split into two separate storylines. The first concerns the original World Three and Mr. Wily's plan on finding the Ultimate NetNavi, culminating in the N1 Grand Prix, a NetBattling tournament. At its conclusion, the Ultimate NetNavi PharaohMan awakens from his slumber and proceeds to claim the net as his own, deleting MegaMan in the process. PharaohMan would eventually be weakened by the two tournament finalists, ProtoMan and a newly rebuilt MegaMan with Style Change option, leading to his capture by Wily. The second half of the season has the characters take on Grave, a NetMafia syndicate spearheaded by Wily that seeks to create a virus beast with the capability to destroy the net.
Months later, Lan's father Dr. Yuichiro Hikari completes his research on the Synchro Chip, a device that enables Operators and NetNavis to become one through the use of Cross Fusion. This development coincides with a plot by Nebula (led by the notorious Dr. Regal) and the Darkloids to take over both the human and cyberworlds. Lan manages to use the then-untested Synchro Chip to Cross Fuse with MegaMan and defeat the Darkloids that materialize in the real world with the aid of Dimensional Area Generators. Because of this, Lan is invited to become a NetSaver (Net Savior), an Official NetBattler charged with protecting the net. As a result of Cross Fusion, MegaMan loses his Style Change option, but instead gains the ability to use Double Soul (Soul Unison) with which allows him to combine his powers with other NetNavis.
Following the end of Axess, Duo, a being from outer space who seeks to destroy humanity after witnessing the chaos caused by Dr. Regal, appears. Intrigued by Cross Fusion, he decides to spare mankind temporarily, bestowing a test upon the main characters to assess whether or not humans truly merit survival. He sends his subordinate, Slur, to Earth, where she hands Navis possessing the powers of Duo's asteroid to unsuspecting people to observe what they will do with such might. Lan and the other net saviors must work together to foil Duo and his subordinate.
