secret weapon: Shadow Rifle  -  Beat "Last Story".

Egg Vacuum  -  Clear neutrals mode/get all chaos emeralds

Last Story  -  Beat every 6th stage in story mode, and see the hero and dark endings for each. (10 endings in all)

Expert Mode  -  Get all 71 "A" rankings.

Heal Cannon - Successfully complete the Hero storyline to unlock the Heal Cannon.

Omochao Gun - Successfully complete the Semi Hero storyline to unlock the Omochao Gun.

Samurai Blade - Successfully complete the Dark storyline to unlock the Samurai Blade.

Satellite Laser - Successfully complete the Semi Dark storyline to unlock the Satellite Laser.

Level 2 weapons - Successfully complete both the Hero and Dark versions of a storyline to unlock the Level 2 weapons.

All Hail Shadow song -  Successfully complete the Hero storyline to unlock the All Hail Shadow song.

All Of Me song (full version) - Successfully complete the Last Story to unlock the All Of Me song (full version).

Almost Dead song - Successfully complete the Dark storyline to unlock the Almost Dead song.

Chosen One song - Successfully complete the Semi Hero storyline to unlock the Chosen One song.

Never Turn Back song - Successfully complete the Dark storyline to unlock the Never Turn Back song.

Library sequences - Successfully complete the indicated type of Story mode missions to unlock the corresponding intermission sequences at the Library:

A Missive From 50 Years Ago (326): Six Hero missions (Hero final Boss)
A New Empire's Beginning (164): Six Neutral missions (Hero final Boss)
Compensation For A Miracle (182): Two Neutral, one Neutral, three Neutral (Hero final Boss)
Faith Taken From Solitude (146): Two Neutral, one Dark, Three Neutral (Hero final Boss)
Punishment, Thy Name Is Ruin (001): Six Dark missions (Dark final Boss)

Two Player mode - Use controller two to play as the Hero characters, such as Sonic, Tails, Knuckles, etc. This also works with Maria, but does not work with Doom's Eye. Note: They cannot pick up guns.

Character choices - In most stages you have three choices: to help the Dark side, yourself, or the Hero side whenever you have someone with you and it is not a Boss fight. To change the character you want with you, press Start. There will most likely be three selections: Dark, Neutral, and Hero. Press Left or Right to highlight a character or ring in the middle. Press A to select the highlighted character. That character will remain with you until your next run in with the other character. You can then simply press Start and do the process again. Note: You cannot select a Hero partner if there is an "X" over the Hero side. You cannot select a Dark partner if there is an "X" over the Dark side. You can also use the D-Pad to change your partner. Press Right for the Hero character, Left for the Dark character, and Down for the Neutral character.

Yuji Naka reference - Sometimes the GUN soldiers will say odd things. One of the things that they say is "Mr. Yuji Naka is all right." Yuji Naka is the creator of the Sonic series.