There are five different types of Matter Gun in the game that are identified by the colours: blue, green, yellow, red, and black. The Matter Guns add features progressively in the respective order. The player begins the game without any tools and must complete puzzles to collect the Matter Gun and later upgraded versions.
A Matter Gun can pick up any cube regardless of it's colour but Cubes stored in a Matter Gun will be changed to the colour of the gun. A Matter Gun can be used to store an unlimited number of cubes, but cannot create or destroy cubes on its own.
All cubes stored in a Matter Gun will be destroyed upon entering a Disintegrator Field.
The Blue Matter Gun is the first and most basic form of Matter Gun. This Matter Gun provides the player with the ability to collect and place Cubes.
The Green Gun allows the player to place cubes in rapid succession even in places normally inaccessible to the player (for example in slits in walls). It also unlocks the an ability known as Cube Farming.
Cube Farming is a method of creating additional Cubes by placing cubes to create the edges of a 2D shape or the frame of a 3D shape. The game creates additional cubes by filling in all the inner cubes to form a solid shape. The additional cubes can then be taken for later use. The process of cube farming is intended behaviour of the game and required to solve many levels.
Oddly, the green gun and the yellow gun are always seen in The Butterfly Effect regardless if the player has taken them or not.
The Yellow Gun adds the ability to move the Cubes around without the need to pick them up and place them back. This allows them to be moved through Yellow Disintegrator Fields. The yellow gun fades between two colors, lime and orange, making it appear yellow when wielded, even though it is actually yellow when it is on the stand. Oddly, this gun and the green gun are always seen in The Butterfly Effect regardless if the player has taken them or not.
The Red Gun allows the player to create walls of Cubes with ease, as well as collect collected Cubes from one point. Be careful though, as creating too large of a wall will crash anyone's game, no matter how good the computer is. The Cubes will be placed radially from the place pointed by the player, starting with the closed unoccupied space. The Cubes will be collected from the furthest point away from the place pointer by the player. The Red Gun allows easy multiplication of Cubes. Having only two cubes the player is able to create any number of them, as placing a whole ring of new Cubes consumes one Cube, while gathering the same ring back gives the player the total amount of Cubes that disappeared. The Red Gun will always appear when mirrored at either Climbing The Tower #7 or The Highest Point even if has been obtained earlier.
Black Gun (Dark Gun)Edit
The Black Gun is only used at the end of the game to carry the Black Ghost.
It is not actually "picked up" as the other guns are - when you pick up the Black Ghost the gun you are using turns black. This gun does not seem to have any special properties other than holding the Black Ghost. After beating the game you retain the red gun. If you press Esc before completely sucking up the Black Ghost, and then click on a different room, you can use the black gun in other areas. You will be set back to the red gun upon restarting the game. Be warned though, using this trick will send you back to the Main Hub just before completing the game.
The "blackgun" is separate in the game files from the "darkgun." The Black Gun is used to place black cubes and works identically to the Red Gun, while the Dark Gun is used to place the Black Ghost. If the in-game console is used to unlock the dark gun, it can be used outside of The End to place many iterations of the Black Ghost around the map.