Lan and his friends are still Pat's village, getting ready to depart for the Dimensional Area Laboratory where Trill was born. After breakfast, the group thanked Pat and the villagers for all the help she had gave them during their stay, including giving them food for their travel. Dingo decides to lead the group to their destination using his tomahawk but by the time it had landed, he was already left behind. Meanwhile, at Gregar's base, Zoano JapanMan was informed of Zoano DarkMan's defeat and promised Gregar that he will avenge his comrade's defeat and capture Trill with his army. Back at Pat's village, Maylu and Chaud arrived and was informed that Lan and the others had already left a few hours ago. After realizing where are they heading, the two of them decides to catch up.
Meanwhile, Lan's group had been hiking up a hill for several hours, with Lan and Dingo already tired. Once they reached the summit, the group decided to take a short break before they continue their journey. While Trill is playing a prank on Dingo, Lan and Raika had a conversation with Iris. Iris apologize to Lan and his friends for getting them involved with the war and pulling them into her world, separating them from their friends and family. Raika encourage her that it wasn't her fault that they ended up in Beyondard and guarantee her that they will help her defeat the Cybeasts. Lan asked Iris about her family and she mentions of her brother. Suddenly, Lan received a transmission from his father but the signal was too poor and they were cut off before Dr. Hikari can tell them anything.
In the original world, Dr. Hikari was disappointed that they failed yet again to send a message to Lan but refuse to give up. Just then, Superintendent Manabe request a Dimensional Area to be activated at her location. It was revealed that even after Lan and his friends were sucked into the Fossa Ambience, Zoanoroids are still being send to wreck havoc in the real world using the CopyBot. With Lan, Chaud and Raika absent, the only thing they can do to combat the Zoanoroids are the Battle Chip Gate and the anti-CopyBot weapon that Makoto created. With the increased in Zoanoroids attacks, Commissioner Kifune request that Dr. Hikari summon the remaining Cross Fusion Members to help them to save the world again.
Back in Beyondard, Chaud and Maylu are able to hitch a ride on a ferry in order to catch up with Lan and the others. The ferryman tell them about how the river was controlled by Captain Blackbeard until recently. Chaud and Maylu immediately know that it must be Lan and the others that had defeat the evil tyrant and restore peace around the lake. Returning to Lan's friends, they continue to travel to a vast desert that Trill was able to remember. Suddenly, SearchMan alert the group that something is approaching them. Zoano JapanMan and his army reveals themselves from beneath the sand and demand that the heroes surrender Trill to them. The heroes immediately summon their Navis to combat the Zoanoroid army. While SearchMan and TomahawkMan handle the foot soldiers, MegaMan engage Zoano JapanMan in combat and manage to injure him by firing a Mega Cannon at point blank range.
During the midst, Iris manage to save Lan from a soldier but was shot in the back. As Lan check up on Iris, MegaMan was defeated by Zoano JapanMan and manage to grab hold on Trill. Before he could get away, Chaud and Maylu had finally catch up and send their Navis to save Trill. The reunion between the heroes had to be put on hold as Zoano JapanMan transform into his Beast Form, now wielding two large katanas. With their opponent being too strong for them to handle, Iris uses her power to fuse MegaMan with Trill, transforming him into Beast Out Gregar. MegaMan make short work off Zoano JapanMan and defeat the remaining army. Once the battle is over, Iris loses conscious and disappear, with a CopyBot remaining in her place before it too dematerialized.
Back in their original world, Tory inform Dr. Hikari about the communication device belonging to Zoano FreezeMan might be able to help them communicate with Lan. After IceMan retrieve it, Dr. Hikari explain that although the device is damaged, they will be able to send a message to Lan if they repair it. Back in Beyondard, Lan and his friends finally reach the Dimensional Area Laboratory to find it abandoned and deserted. Suddenly, the power turn on and a voice welcome the heroes to the lab and direct them to the command room. There, the heroes watched a video showing the day the failed Dimensional Area experiment occur as a result of a virus attack on the lab, leading to the Great Change and the world Beyondard is today. The voice reveals himself to be a computer containing the remaining conscious of the Beyondard version of Tadashi Hikari, Lan's grandfather. He was updated of the heroes identity and what they did until now by Iris' Navi who turned out to be Iris' true Navi form. Iris reveals that her brother was none other than Colonel. Dr. Hikari explained that after Baryl requested to remove some of Colonel's data, Dr. Hikari uses them to create Iris instead of disposing them. The CopyBot that Iris uses was created by Dr. Hikari and is unique compare to the CopyBots that the Zoanoroid uses as this one is able to convert itself into both digital form and material form, allowing the Navi to go in and out of the CyberWorld.
Returning to their main topic, Dr. Hikari reveals the main culprit behind the sabotage of the Dimensional Area experiment is none other than his long time rival, Lord Wily. Using the Dimensional Area, Wily is able to spread the Beast Factor throughout the world and created Gregar and Falzar to battle each other. Whichever Beast left standing will absorb the others body to create an even stronger Super Cybeast. The same effect also works on the Zoanoroid, with each one defeated will make the Cybeasts stronger. Wily plan to download his conscious into the Super Cybeast in order to resurrect himself and to take over both worlds. Knowing of Wily's intentions, Dr. Hikari created the Synchronizer who carries the power to change the world back into its original state. Iris was tasked to take care of Trill until he escaped from the lab and ended up at Lan's world. Around the same time, Gregar and Falzar forces attacked the lab in order to look for Trill. Due to the attack, the computer begin to lose signal. Dr. Hikari entrust the heroes to send Trill to Lord Wily's lab and end the war before disappearing though he is able to give a final smile to Lan, happy to see his grandson from a another world.
Outside, Iris had a conversation with Lan and apologize to him for lying about her true identity. Lan tell her not to worry and human or Navi, she is his friend. Lan explain that he was surprised to see his grandfather in this world. Since Trill was created by his grandfather and MegaMan was created by his father using his grandfather's technology, the same history between the two is the reason why Trill bonded with MegaMan easily. Just then, they saw a figure walking towards the lab. The person revealed to be a heavily injured Baryl who tells them that the enemy had Colonel. As Baryl loses conscious, Iris picked up his Beast Link Gate and lament the loss of her brother.
- Dex Oyama
- Yai Ayanokoji
- Tory Froid
- Dr. Hikari
- Mr. Famous
- Rei Manabe
- Seishin Kifune
- Baryl (Beyondard)
- Colonel (Beyondard)
- Pat Fahran
- Zoano JapanMan
- Lord Wily (Beyondard)
- Tadashi Hikari (Beyondard)
|MegaMan NT Warrior|
| MegaMan NT Warrior • MegaMan NT Warrior Axess|
Rockman.EXE Stream • Rockman.EXE Beast • Rockman.EXE Beast+
Rockman.EXE: Program of Light and Dark
|MegaMan NT Warrior|
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MegaMan NT Warrior Axess
|MegaMan NT Warrior (manga) • Characters • Battle Chips|