When you beat all the ending story boss's the last story will become available.

To unlock the game's expert mode, get an A grade (a "perfect" as quoted by Shadow) on all stages in all missions as well as all boss fights.

To beat the giant tank you fight after completing that level in the Ark where you can kill all the troops, find the professor or save all the scientists, homing attack the guns on it.

Once one's destroyed, pick up the bazooka and use it to destroy another gun on it. Then dodge the plasma blast by either jumping up onto the platform or dropping down onto the floor.

Samurai Sword: Complete the game on the pure evil final mission (the one at the top) and follow any ally. Defeat the boss that follows (Sonic and Diablon if you took evil mission, Black Doom if you took hero mission).

Satellite gun: Complete on the semi-evil final mission with any ally. Defeat the boss (Sonic and Diablon if you took evil mission, Black Doom if you took hero mission).

Egg Vacuum: Complete on the normal final mission with any ally. Defeat the Egg Dealer (same with both missions).

Omachao Gun: Complete on the semi-hero final mission with any ally. Defeat the boss (Egg Dealer if you took evil mission, Black Doom if you took hero mission).

Heal Cannon: Complete on pure hero final mission with any ally. Defeat the boss (Sonic and Diablon if you took evil mission, Black Doom if you took hero mission).

Shadow Sniper: Complete Last Story

Lv. 2 weapons: Complete each final mission with the ally you didn't team up with the first time (e.g. If you took the hero mission on the pure evil mission the first time, take the dark mission the second time to unlock the Lv.2 Samurai Blade). Defeat the final boss. The Shadow Sniper cannot be upgraded.

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Last Story: View all 10 endings

During the levels related to flashbacks of shadows past, like Lost Impact, or the doom.

You will hear some of gun's creeps say things in the back ground like: "they got Keith" or "Mr. Yuji Naka is alright" ; if you haven't figured it out already, Yuji Naka is the producer, and Keith is actually a reference to Keith Palmer, the CG movie producer. Another one mention I believe is "Chris" or Chris Mowry, the Creative services manager.

There are other's mentioned, but I can't remember all of them...

This is Eggman saying to Remember, "it's just a game"

When your like glowing red our blue trie to get a gun and shooht then look at your ameo.

This is the best weapon you could use.

It's the shadow rifle!to get it you need to beat last story.

To unlock you need to fight all of the final bosses of the stories.

Oh yeah the shadow rifle kills just about everything in one shot and you get 20 bullets a time.

Once you beat the final boss of a story line, you get to see a short cutscene of what Shadow would do if he chose this path. Here are some of the endings:
1) Shadow goes bad and rules the world
2) Shadow goes worse and rules the Universe
3) Shadow goes 100% evil and BLOWS UP the World (you don't get to see it though. Bummer.)
4) Shadow goes neutral and rules an army of androids to conquer the earth.
5) Shadow goes neutral and uses the chaos emeralds for his own power
6) Shadow goes good and just mopes around knowing that he was built for evil.
7) Shadow goes good and defeats Balck Doom.
8) Shadow goes 100% hero and Destroys all the Black aliens with Black Doom.
EXTRA INFO
1-3) Shadow destroys Sonic
4-5) Shadow EXECUTES eggman (It's totally AWESOME!)
6-8) Shadow Beats Black Doom
After you beat the last story, Shadow destroys the BlackComet with the eclipse cannon and the world lived happily ever after. By the way, There's a secret about Shadow that you find out by going all neutral, but you can find that one out for yourself.

Once you complete a story line, you unlock a new weapon. If you complete both light and dark missions an end level, then the weapon you previously unlocked on that level will be upgraded to level 2, which will give it more ammo or more power or something. These are the secret weapons:

Samuri Sword-- 4 ammo and fires a thin beam. Upgrade--?
Egg Vaccuum-- Can suck up 25 things when upgraded. Once full, you get free lives and stuff.
Satellite Gun-- You know the first level where lazers come down from the sky? You can aim it!
Omachao Gun-- If you remember him from sonic 2, you fire mini omachaos at enemies. Heal Cannon-- BORING. All it does is revive dead GUN soldiers.

Shadow Rifle-- It's nearly impossible to get, but it is a super strong lazer cannon and looks totally awesome!!! However, you have to have seen every ending and beaten the "Last Story" in order to get it. Personally, I think It's worth it.