So... is Rockman.EXE finished or not?
NO, it is not finished.
Why?
The anime finished after the manga:
Anime finished: September 30, 2006
Manga finished: August 15, 2006
... But MangaUpdates contains information about the anime adaptation and indicates that it is incomplete.
Watching Order (by release date)
Here you have all the anime relations we detected ordered by release date, so you can see the reason for this status in context and also use it as watching order.
The mangas and the non-core contents are excluded by default, but you can enable them by clicking the buttons below:
Rockman.EXE
MegaMan NT Warrior
Anime - Base
Release date: March 04, 2002
Rockman.EXE Axess
MegaMan NT Warrior: Axess
Anime - Sequel
Release date: October 04, 2003
Rockman.EXE Stream
ロックマンエグゼStream
Anime - Sequel
Release date: October 02, 2004
Rockman.EXE Beast
ロックマン エグゼ ＢＥＡＳＴ
Anime - Sequel
Release date: October 01, 2005
Rockman.EXE Beast+
ロックマンエグゼビースト+（プラス）
Anime - Sequel
Release date: April 08, 2006
Synopsis
In a futuristic world, young Netto Hikari receives Rockman, a personalized NetNavi, as he starts fifth grade. NetNavis assist their operators from within their PET devices, and Net Battles are a popular form of competition.
The anime follows Netto and Rockman's adventures as they navigate this digital world, forming a strong friendship and likely facing challenges related to Net Battles and the responsibilities of having a NetNavi.