Special Mode

This is unlocked after completing the game.

Time Attack/Speedrun

Exactly what it sounds like. You speedrun any stage in the game. You are given the Mega Buster, and all of the robot master weapons except for Hell Wheel. No Rush, Wire, or Balloon.

The Mechanical Arena

You unlock this mode by clearing the game with a 15/15 score in Friends.

A Kirby-style boss rush mode on the game's normal difficulty. You must fight all eight robot masters and all Cossack/Wily stage bosses. You are given the Mega Buster and all robot master weapons. You start with 4 E-Tanks. There are four healing pellets in the lobby which heal all of your life, as well as Eddie, who will give you an item in between each boss. 1-Ups exist in this mode, but do nothing; the first time you die, it's over. Don't forget to get the Skull Amulet from Skull Man.

Limited Arena

This is unlocked after completing the Mechanical Arena.

This is actually nine different arenas; It's a boss rush mode where you are given 9 E-Tanks and only one weapon. You can refill this weapon at any time by pressing the Start button. Some of the bosses are immune to some of the weapons, so these bosses are skipped. Each of these is much more challenging than the Mechanical Arena. The easiest one may be the Toad limited arena.

The True Arena

After completing any one Limited Arena, this is unlocked. The True Arena is set to Hard Mode, and is much longer than the Mechanical Arena, containing ALL of the game's bosses and minibosses, as well as a few group fights against ordinary enemies. You do get 9 E-Tanks, though. The True Arena ends with a battle against Cockroach Omega, an extremely difficult super-boss which is exclusive to this mode and My Arena. Bright may be the best weapon to use against this boss.

The fights in the True Arena are divided into several groups. The order in which bosses are fought in a group is random, but you always fight all of the bosses in one group before moving on to the next group.

The first group is the minor minibosses.
The second group is the eight robot master.
The third group is the major minibosses.
The fourth group is the Wily and Cossack stage bosses.
The final group is Optical Capsule, then Super Shadow Man, then Cockroach Omega. You always fight these three bosses in this order.

My Arena

You unlock this by clearing any Limited Arena.

This mode allows you to configure an arena any way you want, choosing which weapons you are given, which bosses you fight, and much more.

Here's a quick primer for those of you who aren't programmers: 0 means off and 1 means on. If you want to turn an option on, set it to one; if you want to turn it off, set it to 0.

The WEAPON option controls what weapons Mega Man gets. See the table below.

The BOSS options determine which bosses are fought in the Arena. See the table below.

The INTERVAL options determine what appears in the rest area between fights. The first four options control whether the full-health pellets in each corner appear.

The RAND. options are as follows:

00: Fight all of the bosses in a predetermined order.
01: Fight all of the bosses in a random order.
10: Fight all of the bosses in a random order, but the last bosses are fixed.
11: The order of bosses within groups is shuffled, but the groups are fought in order. As with the True Arena, the game's final three bosses are fought in a fixed order at the end.

The EQUIPM. option determines what equipment Mega Man gets.

The TANK option determines how many energy tanks you start with. For programmers, this is a binary numbers. For everyone else, basically, you can turn on more than one of them, and they will add together. If you want to give the player 9 E-Tanks, for example, turn on "8 E-Tanks" and "1 E-Tank". You can use different combinations to add up to any number between 0 and 15 E-Tanks. You can exceed the standard limit of 9 E-Tanks to get up to 15, it just won't display correctly. Why's that useless tens digit there, anyway?

The LIFE RCV. option determines how much health you get after each fight. This is a binary number, just like E-Tanks, as described above. You can set any value between 0 and 31. Mega Man has 28 health so setting it any higher than 27 doesn't do anything different.

The EN. GEN. option determines whether Mega Man gets the energy charger.

The E. RFL. AT PAUSE option determines whether your weapon energy comes back when you pause, like in the Limited Arena.

The CRIT option turns critical hits on and off.

The SHORT INV. option makes it so enemies have short invincibility durations.

Audio Player

You unlock this by clearing any Limited Arena. It's a sound test.

Configuration

This takes you to the normal configuration menu.

Extra Configuration

You unlock this by clearing any Limited Arena. It lets you just make whatever save data you want.

STAGE: which stage you're on:

00000000: Bright Man
00000001: Toad Man
00000010: Drill Man
00000011: Pharaoh Man
00000100: Ring Man
00000101: Dust Man
00000110: Dive Man
00000111: Skull Man
00001000: Cossack 1
00001001: Cossack 2
00001010: Cossack 3
00001011: Cossack 4
00001100: Wily 1
00001101: Wily 2
00001110: Wily 3
00001111: Wily 4
All others: Glitch

C.P.: which checkpoint you're at in a stage.

00000000: Beginning of stage
00000001: First checkpoint
00000010: Second checkpoint
All others: Glitch

CLEAR: Which stages you have beaten. The first switches correspond to the following stages, from left to right:

Skull Man
Dive Man
Dust Man
Ring Man
Pharaoh Man
Drill Man
Toad Man
Bright Man

To set which Cossack/Wily stages you've completed, set the left hand side to 11111111 (all robot master stages completed), then set the right hand side to the following values:

00000000: Cossack 1
00000001: Cossack 2
00000011: Cossack 3
00000111: Cossack 4
00001111: Wily 1
00011111: Wily 2
00111111: Wily 3
01111111: Wily 4

WPN: Which weapons you have. The layout is the same as the My Arena setting described above.

LIVES: The number of remaining lives as a binary number. Setting it higher than 9 is allowed, but it won't display properly.

TANK: The number of E-Tanks as a binary number. Setting it higher than 9 is allowed, but it won't display properly.

EQUIPMENT: The equipment Mega Man has. The order is described by the "tool tip" in the game.

TML: Too many lives. This is a cheat setting. Turn this on for infinite lives. 00000000 is off, any other value is on.

C.RFL: This is a cheat setting. Recover weapon energy when paused, like in the Limited Arena. 00000000 is off, any other value is on.

EXWP: This is a cheat setting that lets you bring a special weapon to any stage.

00000001: Quint's Sakugarne (doesn't work properly)
00000010: Enker's Mirror Buster
00000011: Joe Armor
00000100: Joe Copter
00000101: Joe Cannon
00000110: Joe PWC
00000111: Joe Spaceship
00001000: Punk's Screw Crusher
00001001: Ballade's Ballade Cracker
00001010: Terra's Spark Chaser
00001011: Wily Buster

PROG: A setting that has something to do with game progress. Apparently, this doesn't do much.

FLAG: Sets special game conditions. Again, set to 0 for no, 1 for yes. In order, left to right:

Eddie killed
Beat saved
Kalinka saved
Toad Man turned into a toad and spared in Wily 3
Rush saved
The player has ever re-entered a robot master stage (Generally better to leave this off, as it deducts from your score at the end of the game)
The player has ever taken damage (Leave this off to fight Super Shadow Man in Wily 4)
(Unused)

S.VAL: These flags do different things on different stages. Puresabe's documentation doesn't even try to explain all of it.

Records

Shows your speed records in the main game and the special modes.

Trophies

These are achievements, basically.

1. ??? - Clear the game with a Hero Score of 100.

2. Hard Rock - Clear Hard Mode without getting a game over. I don't know if this means setting the preset to Hard or just setting the Main setting to Hard. I unlocked it on the Hard preset.

3. Proof of Omega - Clear the True Arena.