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Most NetNavi characters have their operators visible in the background, following them, either in person like the Pokémon Trainer in Super Smash Bros. Brawl or as a floating screen showing the character. The reverse may be done too, but as a small hologram like Rockman.EXE Beast and only for main characters.

Main Characters

MegaMan Default MegaMan, only having what he had in the first game.
MegaMan (Style Change) MegaMan with Style Change. Unlocked by finishing the main game mode with MegaMan.
MegaMan (Double Soul) MegaMan with Double Soul. His transformation depends on the Battle Chip used to activate it. Unlocked by finishing the main game mode with MegaMan.
Bass Cross MegaMan Starts as normal MegaMan, becoming Bass Cross MegaMan by using his Hyper Combo. Unlocked by finishing the main game mode with MegaMan.
MegaMan (Cross System) MegaMan with a Cybeast and the Cross System. Unlocked by finishing the main game mode with MegaMan.
Mega Man (Trans Arm) MegaMan with Trans Arm. Unlocked by finishing the main game mode with MegaMan.
Dark MegaMan The only version that can use Dark Chips. Unlocked by finishing the main game mode with MegaMan (Double Soul).
MegaMan (Full Power) MegaMan with all customization options available for him. Not allowed in multiplayer modes, except for the "Free for All" mode. Unlocked by finishing the main game mode with MegaMan (Double Soul) and MegaMan (Cross System).
ProtoMan
Dark ProtoMan Can use Dark Chips.
Bass.EXE
Bass GS
Bass (Falzar) Bass with the power of the Cybeast Falzar.
Bass (Full Power) Not allowed in multiplayer modes, except "Free for All".
Roll
GutsMan
Glide
NumberMan
Colonel
Iris
Mr. Prog Assist character that functions like the Servbots from Mega Man Legends, calling more Mr. Progs to assist. Has the lowest overall stats from the Mega Man Battle Network characters, but is also the smallest character, being harder to hit. Alternate colors are blue, pink, red, white, and golden.
NormalNavi Default good guy (although his bad version is one of his colors). Common in virtual scenarios.
HeelNavi Default bad guy. Common enemies in virtual scenarios.
Lackey A Nebula lackey. Common enemies in real world scenarios.
HeelNavi (B) The Mega Man Battle Network 6 version. Advanced enemies that appear in both real and virtual worlds due to the CopyBots.

Mega Man Battle Network

FireMan
ElecMan
ColorMan
MagicMan
IceMan
SharkMan
WoodMan
SkullMan
ShadowMan
PharaohMan
Life Virus Not allowed in multiplayer modes, except "Free for All".

Mega Man Battle Network 2

AirMan
QuickMan
CutMan
KnightMan
MagnetMan
FreezeMan
NapalmMan
PlanetMan
ToadMan
HeatMan
ThunderMan
SnakeMan
GateMan
Gospel Not allowed in multiplayer modes, except "Free for All".

Mega Man Battle Network 3

FlashMan
BubbleMan
DesertMan
FlameMan
PlantMan
MetalMan
MistMan
BowlMan
Punk
DarkMan
YamatoMan
Alpha Not allowed in multiplayer modes, except "Free for All".
Serenade
Serenade (Full Power) Not allowed in multiplayer modes, except "Free for All".

Mega Man Battle Network 4

AquaMan
BurnerMan
ColdMan
JunkMan
KendoMan
SearchMan
SparkMan
TopMan
VideoMan
WindMan
ShadeMan
LaserMan
Duo Not allowed in multiplayer modes, except "Free for All".

Mega Man Battle Network 5

TomahawkMan
GyroMan
Meddy
LarkMan
GridMan
BlizzardMan
CloudMan
CosmoMan
Nebula Grey Not allowed in multiplayer modes, except "Free for All".
Chaos Lord Not allowed in multiplayer modes, except "Free for All".

Mega Man Battle Network 6

B
Gregar Can't be used in multiplayer modes, except "Free for All".
Falzar Can't be used in multiplayer modes, except "Free for All".

Other games

StarMan
GravityMan
SwordMan
Zero
HatMan
JammingMan
Cache
RideMan
Trojan
ClockMan

DLCs

CharacterDetails
Sol Cross MegaMan Part of the Konami DLC pack.
C.F.MegaMan Part of the Anime DLC Pack.
C.F.ProtoMan Part of the Anime DLC Pack.
C.F.Dark ProtoMan Part of the Anime DLC Pack.
C.F.Roll Part of the Anime DLC Pack.
C.F.Colonel Part of the Anime DLC Pack.
C.F.GyroMan Part of the Anime DLC Pack.
C.F.KnightMan Part of the Anime DLC Pack.
C.F.MagnetMan Part of the Anime DLC Pack.
C.F.Meddy Part of the Anime DLC Pack.
C.F.NapalmMan Part of the Anime DLC Pack.
C.F.NeedleMan Part of the Anime DLC Pack.
C.F.ShadowMan Part of the Anime DLC Pack.
C.F.SearchMan Part of the Anime DLC Pack.
C.F.TomahawkMan Part of the Anime DLC Pack.
C.F.PrismMan Part of the Anime DLC Pack.
C.F.LaserMan Part of the Anime DLC Pack.
C.F.CircusMan Part of the Anime DLC Pack.
C.F.DiveMan Part of the Anime DLC Pack.
Dr. Regal Part of the Anime DLC Pack.
GreenMan Part of the Anime DLC Pack.
LeagueMan Part of the Anime DLC Pack.
NoodleMan Part of the Anime DLC Pack. Can shapeshift, but his pallette remains the same.
PickMan Part of the Anime DLC Pack.
DrillMach Part of the Anime DLC Pack.
RocketMan Part of the Anime DLC Pack.
ShiningMan Part of the Anime DLC Pack.
WhaleMan Part of the Anime DLC Pack.
Sledgehammer Brothers Part of the Anime DLC Pack. Act together like the Ice Climbers in Super Smash Bros.
PrismMan Part of the Anime DLC Pack.
Silk Part of the Anime DLC Pack.
Slur Part of the Anime DLC Pack. Can't be used in multiplayer matches, except for "Free for All".
IgoMan Part of the Anime DLC Pack.
ShogiMan Part of the Anime DLC Pack.
GateballMan Part of the Anime DLC Pack.
ShiatsuMan Part of the Anime DLC Pack.
ShuutomeMan Part of the Anime DLC Pack.
Super Cybeast Part of the Anime DLC Pack. Can't be used in multiplayer matches, except for "Free for All".
Rhythm Part of the Manga DLC Pack.
Bugriser Part of the Manga DLC Pack. Can't be used in multiplayer matches, except for "Free for All".