Mega Man X: Command Mission Cheats

Action figures:
Go to the North Square of Central Tower. Enter one of the following passwords at the special figure slot to get the corresponding prize.

Axl: 38184155 or 44527839 (Japanese version)
Axl (DNA changing pose): 91327856 or 46925056 (Japanese version)
Cinnamon: 92106548 or 10950508 (Japanese version)
Cinnamon (Iron Maiden): 31415926 (Japanese version)
Marino: 02098772 or 20040729 (Japanese version)
Marino (Quicksilver): 19780506 (Japanese version)
Massimo (Dymonion): 47722361 or 82536252 (Japanese version)
Mega Man X: 73001472 or 19670801 (Japanese version)
Mega Man X (victory pose): 44162918 or 78523511 (Japanese version)
X-Armor: 19690831 or 32603260 (Japanese version)
Zero: 29290141 or 33515937 (Japanese version)
Zero (Black): 72443102 or 69203600 (Japanese version)

Unlock the Classic Mega Man:
To unlock the classic Mega Man, Finish the game. Then, highlight the "Continue" option and press Left(2), Right(2), Left, Right(2), Left(2), Start. That option will turn blue, and you can play as the Original Mega Man.
User Cheat by Man_With_Glasses

Unlock Proto Man:
Finish the game with Zero, depending on your game play. Then, highlight the "Continue" option and press Left, Right(2), Left(3), Right, Start. That option will turn red, and you will get to play as Proto man.

Hard version:
Finish the game, then highlight the "New Game" option. Then, press Right(3), Left(2), Right, Start. That option will turn yellow, and you will now have a hard difficulty setting.

Challenges and rewards:

Fight over 500 battles: Yellow Scarf
Play for 25 hours: Force Metals
Activate over 100 final strikes: Retro Mech figures
Defeat over 100 enemies: Preon Special figures
Defeat over 1,000 enemies: Preon Special 3 figures
Defeat over 500 enemies: Preon Special 2 figures
Get 50 Force Metal recipes: Force Metal ore
Gain over 100,000 experience points: Mini Mech figures
Defeat over 100 Preon series: Preon Army figures
Play game for 10 hours: Justice picture
Talk to citizens over 100 times: Armada picture
Defeat over 100 Enigmas: Preon special figures
Defeat over 100 Mettaurs: Mettaur Special figures
Deploy Mechaniloids over 50 times: Trajectory of Battle 2 music
Use over 100,000 FME in the generator: Cinnamon's Secret picture
Complete deployment recovery: Hunter Base picture
Complete figure sets 1 through 10: The Deadly Trio! picture
Collect all sketches: Purple Scarf
Complete the game: Final Confrontation video
Fight over 100 battles: Yellow Scarf
Collect all video clips: Rafflesian sketch
Buy over forty main weapons: Nana sketch
Collect all Disc files: Dr. Psyche sketch
Fight over 100 battles: Mouse Mecha sketch
Reach level 30 with X: Support Mecha sketch
Collect all ten posters: Proto Crab Mech sketch
Defeat over 100 Preon-type enemies: Preon Army sketch
Get over 100 critical strikes: X Ninja version sketch
Use Action Trigger over 100 times: X Flying version sketch
Collect all field items: Mega Man sketch
Collect all background music files: Duckbill Mole sketch
Get over 150 consecutive hits: X's Armor sketch
Get over 10,000 experience: Water Curtain sketch
Buy over 100 items: Tree Trunk Room sketch
Collect all figure tokens: Glass Passageway sketch
Perform an attack with over 9,999 damage: Guns sketch
Collect all Mechaniloids: Giga City sketch
Save 50 times: Save Process sketch
Play the game for 25 hours: Force Metals sketch
Obtain over 50 Force Metal recipes: Force Metal Ore sketch
Spend over 100,000 Zenny: Teleport Device sketch

Optional Bosses, enemies, and rewards:

Rafflesian (joined by two Belldonnas)
Level: 77
LE: 31500
Power:115
Armor:75
Shield: 65
Speed: 70
Fire Damage: 100%
Water Damage: 100%
Thunder Damage: 100%
Rewards: 10,000 Zenny, 22,000 experience, 3,000 FME
Dropped items: Tank Parts (100%), Figure Token (100%), X's Ultimate Armor (in room)
Steal items: Build LE, Force Tomahawk (both 25%)
REMEMBER: Restores LE and grows a little in power each turn.
Location: Tianna Camp; requires Tianna Key from deployments.

Belldonnas
Level: 44
LE: 20500
Power: 115
Armor: 60
Shield: 60
Speed: 100
Rewards: 2,000 Zenny, 4,000 experience, 600 FME
Dropped items: Turbo Clock, Resist (both 100%)
Steal items: Force Missiles, Build Speed (both 25%)
REMEMBER: Restores LE every turn and grows in attack every time it is attacked.
Location: With Rafflesian

Duckbill Mole
Location: Melda Ore Plant; requires Melda Key from deployment.
REMEMBER: Zero's Extra Hyper mode is in the room.

Onetail
Location: Central Tower 999F shaft; requires Central Key obtained when Chapter 10 is completed.
REMEMBER: Restores about 10,000-20,000 LE each turn.

Twotails
Location: Room after Onetail
REMEMBER: There may be two of them. Element shifter; Analyzer and Force Metal recommended.

Threetails
Location: Room after Twotails.

Fourtails
Dropped items: Zero's Red Lotus Saber (his best weapon)
Location: Room after Threetails.
REMEMBER: Has extreme power and has the same defense as Scarface.

Fivetails
Location: Room after Fourtails, appears in a trio.
REMEMBER: Watch out for self-destruct.

Sixtails
Location: Room after Fivetails.
REMEMBER: Must be defeated before tenth turn, when he fully recovers.

Seventails
Location: Room after Sixtails.
REMEMBER: There are two of them. They recover LE every turn and get stronger every time they are attacked

Eighttails
Location: Room after Seventails.
REMEMBER: There are two of them, have full elemental attack range. When one is defeated the remaining one summons another. After defeating Eighttails, the next room is a special figure token room. Make sure you heal and save for the next battle.

Ninetails
LE:92500
Power:400
Armor: 90
shield: 95
Speed: 140
Drops: DNA strand for Axl and his Ancient Gun weapon
Location: One or two rooms after Eighttails.
REMEMBER: Occasionally uses Regeneration to recover 25% of your party's health. Watch out for the Nine Fragments move, which hits nine times and does 699 to 999 LE damage with each hit. He also recovers over 10,000 LE each turn.

Axl's DNA strands:

Wild Jango: Defeat him in the Central Tower Chapter 2.

Silver Horn: Defeat him in Tianna Camp Chapter 3.

Mad Nautilus: Defeat him in Gaudile's Lab Chapter 4.

Mach Jentra: Defeat him in Ulfat Factory Chapter 5.

Incentas: Defeat him in Gimiala Mine Chapter 6.

Depth Dragoon: Defeat him in Far East HQ Chapter 10.

Raflesian: Defeat her in Tianna camp by using Mechaniloids to get the Tianna key.

Ninetails: Defeat him in Central Tower once you have the Central Key. REMEMBER: To get the Central Key you must complete the game.

Mega Man X: Command Mission FAQs and Guides

Mega Man X: Command Mission Official Website

Mega Man X: Command Mission Review - Silicon ERA