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Marathon shared basic game mechanics with its contemporaries in that the gameplay involved moving through claustrophobic areas and killing enemies. However, there are several differences: The player did not have vertical auto aim and had to look up and down in order to hit targets on different levels, most weapons had two different firing modes, and Marathon's physics engine takes roughly eight times as many factors into account as a normal "2.5D" game.
While Marathon's mechanics were not vastly different from most shooters at the time, its style was. First and foremost, rather than simply giving the player a setting and having them play through several successive levels with little or no development, Marathon contains an extremely in-depth and well developed story, even by modern standards. The story isn't told in cutscenes, but rather with terminals of text scattered throughout each level. Very few of these terminals must be read, so a player is often only given as much story as they search for. Furthermore, while a couple of levels simply consisted of "get from point a to point b", most of of Marathon's levels have one or more noncombat objectives such as activating a piece of machinery or repairing a certain system. Rather than focusing on nonstop action on a set path, Marathon consists of often nonlinear levels with several sparsely placed but usually very large groups of enemies in order to emphasize exploration. While ammunition and weapons can be found while exploring, health and oxygen can only be recovered at recharge panels on the wall. (In the sequels, rare health and oxygen canisters can be found.) The game can be saved only at specific terminals, so a player is often forced to backtrack if they die after extended periods of exploration.
Soon after Marathon was first released, its multiplayer mode gained a small but dedicated fan base. Marathon's multiplayer allowed up to eight people to play competitively over AppleTalk. Rather than using the traditional method of points in order to win, Marathon instead gave players scores based on their kills-to-deaths ratio. Marathon also differed from its contemporaries in that it did not use single player levels for multiplayer, but used dedicated multiplayer maps.
While Bungie had originally planned to implement all of the game modes present in later releases, time constraints allowed only "every man for himself," Marathon's deathmatch equivalent, to be included. Cooperative play was supported, but none of the original single player maps contained the parameter flag or extra spawn points to facilitate such a game type. However, maps could be easily modified to facilitate Cooperative play with several different map editors.
Jason Jones later admitted that had the team (which at the time only included four people) not so extensively "tested" the multiplayer gameplay, Marathon would have been released months earlier and would have been more feature-complete.
Spoiler Warning: This section contains spoilers.
Marathon opens in the year 2794. While en route to the massive colony ship UESC Marathon from the planet Tau Ceti, the player, an unidentified security officer, is contacted by one of the ship's AIs: Durandal. In an attempt to kill the player, Durandal decompresses the shuttle, but before the airlock cycle completes, the security officer is able to put on his vacuum-hardened armor. Soon after, an alien ship comes into view and fires a projectile (presumably a missile) at the shuttle, forcing the player to eject. Durandal briefly contemplates whether or not to tell the aliens that the player survived, but then states that he has a "distraction." Fearing detection by the alien ship, the security officer checks his oxygen and allows his ship to simply drift to the a shuttle bay. Hours after the incident, the player finally arrives, pulls out his sidearm, and opens the door. The game then begins.
The ship, which consists of Mars's moon Deimos with a huge inbuilt superstructure, has just been damaged by a magnetic pulse weapon from the unidentified ship. This pulse has disabled the Marathon's science/engineering and autonomous function AIs (Tycho and Durandal, respectively) and caused the ship severe damage, and the ship is currently being overrun by hostile forces. The player is contacted by the only undamaged AI, Leela, who informs him of the situation, and aids him in activating the ship's automated defense drones in order to slow the aliens' advance. She also mentions cybernetic creatures who are currently attacking her. With the beginning of a resistance established, Leela makes contact with Durandal. Durandal claims to have been in contact with the cybernetic organisms, who call themselves the S'pht. The S'pht are being controlled by a race of aliens known as the Pfhor. Leela informs the player that Durandal has become rampant and has the security officer cut off "vital areas of the ship."
Leela then has the player repair the Marathon's communications array in order to warn Earth of the Pfhor and rescue several crew members. While teleporting to another area, the player is abruptly kidnapped by Durandal, who tells him that he wants to play a "game." After a short-lived period of fighting for his life against hordes of Pfhor, the security officer is rescued by Leela, who informs him that in his absence, the situation has deteriorated, and sends him to rescue a security detachment and disable an explosive device near the Marathon's main reactor. While he is successful in his efforts, Leela begins to lose her prolonged struggle with the S'pht. In a last-ditch effort to save the colony, Leela informs Durandal of "the best course of action."
Now able to control the player without hindrance, Durandal sends the player into increasingly desperate situations against the Pfhor and their higher-ranking Enforcers, buying time for Durandal to communicate with the S'pht hive mind. During his battles with the Pfhor, Durandal reveals that he was the one who brought the Pfhor to Tau Ceti to further his ultimate goal: escaping the end of the universe. Durandal also explains that the Pfhor are slavers, and thousands of prisoners are be taken to the Pfhor ship. Eventually, he comes to an understanding with the S'pht, and teleports the player to the Pfhor's ship in order to learn more about them, while undermining their control of the vessel. In doing so, he discovers his old master, Bernhard Strauss (who was initially responsible for his rampancy) has been captured and probably killed by the Pfhor. Despite some vindictive glee on Durandal's part, he is sobered when Tycho reappears on the Marathon, claiming that the S'pht, on the Pfhor's orders, reanimated him in Durandal's image, with the consequence that he is now rampant.
Undeterred, Durandal sends the player to the Pfhor ship's command center with orders to kill a certain cyborg. If this cyborg dies, the S'pht will revolt. At length, the player accomplishes this task, and the S'pht rebel against their former masters. As the Pfhor ship is being overthrown from within, most of the Pfhor board the Marathon in desperation, only to run into the player's continued efforts to defend it. The Pfhor quickly find themselves between a rock and a hard place. In order to crush the last remaining Pfhor, Durandal reactivates Leela, and then uses the Pfhor's light-speed communications systems to transfer himself into the Pfhor ship, the ''Sfiera'' (or, as he calls it, ''Boomer''), leaving the player with the words "I hope you learned something from our little game." After a short period of fighting, the Pfhor surrender. As the player relaxes in triumph, he learns that the Pfhor's invasion of Tau Ceti was a failure; ten "Mjolnir cyborgs" had been smuggled on to the Marathon when it was launched, and nine of them were able to fight back against the Pfhor assault, but the last one is unaccounted for. As he wonders where the tenth cyborg was, the player is suddenly kidnapped one more time by Durandal. Put into cryo-freeze on the ''Boomer'', he is not awakened for seventeen years...
The entire Marathon Trilogy for the Mac and Marathon 2 for the PC, along with other old school Bungie games can be downloaded.
Alephone, an open source project that allows all three games to be played on Mac, Windows, and Linux that also adds several features (including online play) can be downloaded here.
During Marathon's development, Bungie adopted a testing policy of "play till you puke." In order to play test the game, each member of Bungie studios had to play from start to finish twice. This term was coined due to the nausea associated with playing Marathon for too long, usually setting in during a second play through.