The original Mac OS version of the game and its manual are available to download for free at http://trilogyrelease.bungie.org/. Individual files can also be downloaded as opposed to the full game. The game has also been modified to no longer require serial keys to install. As an added bonus, the ISO for the Windows 95 version is available.
Note that they are provided as is and will only run on a classic Macintosh or Windows 95/98. The Windows version also has some changes in the level design and a secret not present in the Mac OS version. They also have a download for just the windows map file (beneath the iso download) for use with Aleph One or the Mac version.
It is recommended to use the Aleph One version as it adds support for modern systems and bug fixes.
Aleph One is an open source continuation of the Marathon 2 engine. It makes the game more modern and accessible with many different improvements such as cross-platform support, widescreen resolutions, and improved multiplayer networking.
For Windows and OS X, everything is provided as a single app/folder. For Linux, the engine need to be downloaded separately from the game files, compiled, and merged in.
Both the engine and the game files can be downloaded at https://alephone.lhowon.org/.
As a bonus, the game files provided by Aleph One include the HD texture pack used in the Xbox Live Arcade release of Marathon 2: Durandal.
A legal serial key generator for the retail versions of all Marathon games. Refresh the page to get a new batch of keys. Marathon 2: Durandal keys are stated with "M2" before the codes.
It can be found at http://marathon.bungie.org/maraserialgen/.
In-game general OpenGL settings.
In-game advanced OpenGL settings.
<marathon><view><fov normal="120" extra="160" tunnel="70" /></view></marathon>
In-game key map settings.
In-game mouse settings.
In-game joystick settings.