It's been one month since the Dark Chip Syndicate Nebula has attempted to hijack an asteroid to aid in their plan to create a world of darkness, but their plan was foiled by Lan Hikari and his NetNavi MegaMan.EXE. Nebula's back, and this time they've taken over the internet!
- Liberate Mission - A new battle mode that challenges you to defeat certain viruses on the battlefield. Defeating them will allow you to face the boss!
- Teamwork - In this game, you must work together with other navis in order to clear the field of obstacles and face the boss.
- Chaos Unisons - In this game, you can unite with the dark side of navis and fight as one being for one turn!
- Crossover Battle - For the first time in Battle Network history, you can partake in a special "crossover battle" mode by linking up with the Boktai 2 game with a Wireless Adapter.
- 6 new souls to obtain in master in both Team Colonel and Team Protoman, for a total of 12 souls.
- Vision Burst - Find special areas of the internet that contain data from the past to find information useful in completing the game.
This game is also known as Rockman EXE 5: Team of Colonel in Japan.