Action figures
Go to the Figure Vending Machine in Access Tunnel E-1. Enter one of the following passwords at the special figure slot to get the corresponding prize:
Axl: 38184155
Axl (DNA changing pose): 91327856
Cinnamon: 92106548
Cinnamon (Iron Maiden): 19837556
Marino: 02098772
Marino (Quicksilver): 87352041
Massimo (Dymonion): 47722361
Megaman X: 73001472
Megaman X (victory pose): 44162918
X-Armor: 19690831
Zero: 29290141
Zero (Black): 72443102
X's Ultimate Armor
First, get the Tianna Key for the the locked door in the Tianna Camp. Then, go to the locked door and open it. Inside you will fight a Boss that is accompanied by two Belladonnas. Defeat them, and after the fight break the red crystal to get X's Ultimate Armor Hyper Mode.
Lagrano Ruins Key.
To get the Lagrano Ruins Key, you need to use the Deployment Center. Keep deploying your robots until they can find the key. After a few times, you will see it listed on the right-hand side of the screen when you check on the returned robots. After going through the door in Largano Ruins, you will find a secret item/force metal/weapon shop.
Absolute Zero Hyper mode.
First, complete Chapter 8. Then, repeatedly deploy well-chosen units to the Melda Ore Plant in order to gain the Melda Key. Once you gain the key, go to the Melda Ore Plant and open the previously locked door (once you teleport there, go inside the plant and enter the locked door instead of entering the first elevator). Continue through the new area until you encounter a duck-like enemy. Defeat him and break the purple crystal behind him to gain the Absolute Zero Hyper mode. It should not be too difficult to defeat the enemy -- just continue to use X's and Zero's current Hyper Mode and Action Triggers and make sure you do not attack him with an element he is currently absorbing (a message will appear at the top of the screen whenever his absorbing element changes). Defeating this enemy is a lot easier than defeating the enemy which guards X's Second Hyper Mode.
Defeating Preon Nurse
Find a Preon Nurse in any unit. Destroy all enemies except the nurse. When the nurse is the last one remaining, steal its Reboot and Tank Energy 10. While you wait for its turn, keep using Zenny+ attacks on it. After the first turn of the nurse, it will say that it surrenders will use All Life 25 on your party. Then, destroy the nurse in order to get the Zenny bonus that you put on it before it attacks again. If you do not destroy it after it heals you, it will use an attack called "Then Thanks" and run away, giving you nothing.
Challenges and rewards
Buy 100 items: Tree Trunk Room picture
Fight over 100 battles: Mouse Mech picture
Fight over 500 battles: Yellow Scarf
Play for 25 hours: Force Metals
Achieve over 100 critical hits: X ninja version picture
Activate over 100 final strikes: Retro Mech figures
Save over 50 times: Save Process picture
Defeat over 100 Preon series: Preon Army figures
Defeat over 100 enigmas: Preon special figures
Defeat over 500 enemies: Preon Special 2 figures
Get 50 Force Metal recipes: Force Metal ore
Use over 100,000 Zenny: Teleport device picture
Gain over 100,000 experience points: Mini Mech figures
MAX attack over 9,999: X's guns picture
Play game for 10 hours: Justice picture
Talk to citizens over 100 times: Armada picture
Get over 10,000 experience points: Water Curtain picture
Use action trigger over 100 times: X flying version picture
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%)
Note: 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%)
Note: 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.
Note: Zero's Extra Hyper mode is in the room.
Onetail
Location: Central Tower 999F shaft; requires Central Key obtained when Chapter 10 is completed.
Note: Restores about 10,000-20,000 LE each turn.
Twotails
Location: Room after Onetail
Note: 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.
Note: Has extreme power and has the same defense as Scarface.
Fivetails
Location: Room after Fourtails, appears in a trio.
Note: Watch out for self-destruct.
Sixtails
Location: Room after Fivetails.
Note: Must be defeated before tenth turn, when he fully recovers.
Seventails
Location: Room after Sixtails.
Note: There are two of them. They recover LE every turn and get stronger every time they are attacked
Eighttails
Location: Room after Seventails.
Note: 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.

Note: 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.