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Like Gearbox's other expansion packs Opposing Force and Blue Shift, Decay returns to the setting and timeline of the original story, but with different player characters: two female colleagues of Gordon Freeman, Dr. Gina Cross and Dr. Colette Green. Dr. Gina Cross is the model for the Hazard Course hologram, and can be seen at a point in Blue Shift. Dr. Green is a new character invented for Decay.
Although Gearbox completed a PC port of the game, Decay was never released "due to powers beyond Gearbox's control"<ref name="Gbox-letter"> Gearbox note on Decay, .</ref>. As such most Half-Life players never got a chance to play through it. Decay is also not available through Valve's Steam service. Decay is, however, being ported by fans, at http://decay.hl2source.com, <ref name="fanport"> Decay project status, .</ref> for the Half-Life engine in 2006. If successful, they hope to remake it for Source engine.
Dr. Cross and Dr. Green are members of a different team in Black Mesa than Half-Life's protagonist, Gordon Freeman. They are responsible for monitoring the equipment which Gordon uses during the experiment, and are in turn monitored by Dr. Rosenberg (who also appears in Blue Shift) and Dr. Richard Keller. Cross and Green deliver the test sample to Freeman just before the "incident" occurs; like Freeman, they are forced to fight for survival in the aftermath of the resonance cascade. Cross and Green help Rosenberg reach the location he is later found in by Barney Calhoun in Blue Shift. They then proceed to prepare a satellite for launch (an event seen in Half-Life) and subsequently use the satellite in tandem with ground-based equipment to significantly weaken the effects of the resonance cascade. During the conclusion of the game, both characters are caught in what is explained as a "harmonic reflux" by Dr. Keller. It is during this sequence that the voice of Dr. Rosenberg can be heard warning that he "can't keep the portal open much longer," alluding to Calhoun's coinciding trip in Xen during Blue Shift. Dr. Cross and Dr. Green then return safely and Dr. Keller congratulates them on their success. It still remains unclear whether the doctors managed to survive the nuclear explosion that occurs at the end of Opposing Force.
The game storyline is divided into a total of 10 "chapters":
- Dual Access — The experiment must be successful. Monitor the anti-mass spectrometer and deliver anomalous materials to Dr. Freeman.
- Hazardous Course — Survivors must call for help. Escort Dr. Rosenberg through the training area (The Training Facility, Sector A) to the surface.
- Surface Call — To call for help, survivors need active communications. Help Dr. Rosenberg establish an uplink with the outside world.
- Resonance — The rift between Earth and the alien world is widening. Reset the dampening fields to prevent another cascade.
- Domestic Violence — A satellite controls major recovery systems. Locate a security guard who knows the satellite signal codes.
- Code Green — A satellite must be in orbit for recovery systems to operate. Upload the satellite signal codes before the delivery rocket launches.
- Crossfire — Prototype equipment must be used to seal the dimensional rift. Manually raise the displacement beacon into place.
- Intensity — The prototype equipment requires huge amounts of energy. Activate the beam matrix to power the displacement beacon.
- Rift — A resonance reversal may seal the dimensional rift and save the planet. Use the displacement beacon to initiate a reversal.
- Xen Attacks — Two Vortigaunts named drone X-8973 and R-4913 must retrieve the crystal sample which was used in tests in Black Mesa and take it back to their leader Nihilanth.
The player is able to obtain most of the weaponry found in Half-Life excluding the Gauss gun, the Gluon Gun, and the Tranquilizer Crossbow.
Unlike the other narrative-based Half-Life games, which are single player only, Decay is designed for co-operative play. While it can be played by one person, swapping between the roles of Dr. Cross and Dr. Green, the game is intended to be played by two players in split-screen. Various puzzles and combat situations throughout the game require the co-operation of the two characters.
The game is also unique in the context of the Half-Life series by being the only game divided into separate missions, instead of a single unbroken narrative.
Decay has a ranking system for all of its nine missions, ranging from F (worst) to A (best), based on accuracy, number of enemies killed, and damage taken. If all nine missions are achieved with an A level, a bonus mission, Xen Attacks, can be played as a pair of Vortigaunts.
Decay is also the only game of the series where it is possible to fight and defeat a Xen Manta ship, which serves as the final boss.
- Decay was originally called "Hazard Team", but this title was changed so as to fit with rest of the names in the series. The map file names still bear the "ht" prefix.
- In the original Half-Life, Gordon Freeman sees two other empty HEV suit containers when he puts on his hazard suit. These containers are intended to belong to Gina and Colette's HEV suits, who have already taken them by the time Gordon arrives.<ref>http://gbxforums.gearboxsoftware.com/showpost.php?p=2051&postcount=10</ref>
- Half-Life for PS2 includes a code screen in the option menu where cheats can be activated. Two undocumented cheats were discovered by the project leader of Decay's PC port. <ref name="newcheat"> Decay unlock cheat, .</ref><ref name="fanpclead"> PC Decay fan port leader, .</ref> One of these cheats allows the player to unlock all ten Decay missions, including the bonus mission "Xen Attacks". The second cheat causes the game to prompt for an expansion CD. This expansion, consisting of an extra set of bonus levels, was only released on the Sony Underground demo disc of the June 2002 issue of PlayStation Magazine, and was never officially announced. The bonus levels are actually a port of Half-Life: Uplink.
The hidden cheat code to unlock all missions, which requires two controllers to be used, is: p2_R3, p1_L3, p1_up, p1_up, p2_down, p2_down, p1_left, p1_right, p2_left, p2_right, p1_X, p1_O, START. If entered properly, the message "Decay Unlocked" will appear. This button combination is most likely a reference to the Konami Code.