- "Control, this is Bridge, targeting computer has taken control of the helm, cannot override. Repeat: CANNOT OVERRIDE."
Sometime in The Future, Earth is locked in a cold war with an alien race known as the Thanatosians. Somewhere in a classified sector of space, a powerful Human ship — a Cereberus-class vessel known as the SS Jeremiah Obrian — is carrying an extremely powerful weapon to test in war game scenarios.
Enroute to their destination of an uninhabited planet to test their weapon on, the Obrian suddenly alters its course to Calliope, a Thanatosian world. The Obrian plans to unleash the weapon on Calliope, which will trigger a war between Humanity and the Thanatosians which could span the entire galaxy.
The Obrian's crew desperately tries to override the ship's navigational computer but finds that the computer no longer recognizes their DNA and ignores their commands. Now believing them to be intruders, the ship activates its defense mechanism, an armed security drone known as the Defender, which eliminates the crew one-by-one.
None of Earth's other ships are close enough to reach the Obrian before it reaches Calliope. In a last-ditch effort, Earth's military sends out a distress signal across all Human channels, hoping to reach someone, anyone, that can reach the Obrian and stop it. Luckily, a small science vessel known as the Indiana just happened to be drifting by.
Using the Indiana's Tractor Beam, the pilot is able to latch onto the Obrian and send in a remotely-piloted probe to hopefully stop the cruiser from reaching its destination.
Iron Helix provides examples of:
- All There in the Manual: While the in-game cutscenes do a decent job on explaining the story, the manual provides more detail. For instance, the fact that Humanity and the Thanotosians are in a cold war is only mentioned in the manual, not in the game proper.
- Apocalyptic Log: The crew of the Jeremiah Obrian recorded video journals shortly before they were killed by the ship's automated Defender. Finding these journals is required to gain access to the ship's systems.
- Attack Drone: The main, and only, enemy in the entire game is the ship's automated security drone, the Defender, which is constantly patrolling the ship and will kill you on sight.
- Beautiful Void: The entire game takes place onboard the starship Jeremiah Obrian. The interior of the ship looks surprisingly comfy, featuring a lounge, a gym, and several opportunities for stargazing. You are the only living thing onboard since the entire crew was killed by the ship's automated defense drone.
- Biometric Bypass: Access to the ship and the various systems are controlled through DNA scans: if your DNA doesn't match someone on the ship's registry, your access to the ship is severely restricted. The first part of the game involves carefully searching the ship for unmutated DNA of the various crew members, trying to increase your access to the ship until you can get an unmutated sample of the Captain's DNA, which gives you access to everything. Just having access is not enough, though: you still need to figure out how to disable and destroy the ship.
- Cat-and-Mouse Boss: Iron Helix features only a single enemy: the ship's automated security drone, which is unrelenting in its pursuit of you, an intruder, which requires you to never stay in one area for very long or it will find you and kill you. You are only able to stop the drone when you get access to the ship's systems, the exact method of dealing with it changes depending on which difficulty you are playing on.
- Crush. Kill. Destroy!: Unbeknownst to the crew of the Jeremiah Obrian, they were infected with a virus that mutated their DNA, which caused the ship to no longer recognize them or accept their commands. The ship then activated its automated defense drone, which eliminated the crew one-by-one.
- Depopulation Bomb: The titular "Iron Helix" is a biological weapon capable of eliminating all life on a planet with only a single use. Unfortunately, it leaked on the Jeremiah Obrian, and killed everyone on board.
- Featureless Protagonist: By virtue of the player not actually controlling a living, breathing person, but a zoological probe which is merely being remotely-piloted by the protagonist, the game avoids giving any real detail about them. Not even a name or gender. The implication, reinforced by the interface, is that it is you, the player.
- Fling a Light into the Future: The crew of the Jeremiah Obrian knew they were doomed, but that didn't stop them from leaving video logs detailing how to disable the ship's automated defense drone, and how to destroy the ship before it reaches its destination.
- Full Motion Video: Every cutscene is in live-action, though the gameplay is pre-rendered 3D.
- The Future: Iron Helix takes place an unspecified amount of years into the future.
- It's Up to You: You're the captain of a single-pilot biological research vessel on a remote mission, shanghai'd into service to stop the USS Jeremiah Obrian from launching its weapons at a Thanatosian world and igniting a war. You're also the only ship close enough to intercept the Jeremiah Obrian: if you fail, nothing will be able to stop it in time. Also, you have 90 minutes, and no idea what to do.
- Justified Extra Lives: In the form of remotely-controlled probes. You get three of them, if one runs out of power or gets destroyed by the security drone, another will automatically be activated and sent in. Lose all three and, well, Game Over.
- Minimalist Cast: The player character is the only living, breathing person for the vast majority of the game. Other characters do show up, but all but one of them are posthumous characters that you only meet through short video journals.
- Mission Control: Admiral Arboc of Starbase Amethyst is your liaison to Earth's military. She will provide you with relevant info throughout the game.
- Over-the-Top Secret: The very existence of the Iron Helix weapon was so secret that the crew of the ship that was transporting it didn't even know they were transporting it.
- Pop-Star Composer: The ambient, electro-industrial soundtrack was composed by Peter Stone, also known as the one-man musical act Xorcist.
- Posthumous Character: The crew of the Jeremiah Obrian are all dead by the time you get onboard, your interactions with them being limited to discovering video logs they recorded only moments before their deaths.
- Remote Body: The player character never actually steps one foot onboard the Jeremiah Obrian, instead they send a zoological "Darwin 5" probe that can be remote-piloted. The reasons being that a biological weapon was released onboard the ship, and the ship's automated security drone is in a "kill-on-sight" mood.
- Replay Value: The methods of disabling the Defender and destroying the Obrian change with each difficulty level.
- Spell My Name with an "S": The opening cutscene spells the planet's name as "Calliope", while the manual and Game Over screen spell it "Calliopé".
- Sudden Downer Ending: After destroying the Obrian, the player character goes to Starbase Amethyst, only to immediately get detained, interrogated, and tortured by Admiral Arboc, who was helping them throughout the game, but now is demanding to know how much the protagonist knows about "Project: Iron Helix". For some reason, this cutscene is only in the Sega CD version. In the Mac and PC versions, the game simply ends with the player character being summoned to Starbase Amethyst, leaving their fate ambiguous.
- Synthetic Plague: The "Iron Helix" is a biological weapon that attacks the infected's cells, mutating their DNA and rendering their bodies unable to carry out vital metabolic functions, which kills them within only a few hours.
- Timed Mission: You have 90 minutes real-time to stop the Obrian from attacking Calliope. This might sound like a lot of time, but between ducking around the Defender, trying to find the next clue or DNA sample in the chain, having to manage your probe power levels, and the key parts of the ship being rather far apart from each other, you'll likely be running close to the wire if you manage to win.
- Tractor Beam: The Indiana is able to latch onto the Obrian using its tractor beam, which keeps it in tow as the Obrian heads towards Calliope.
- Ungrateful Bastard: Only in the Sega CD version of the game. Even though you just stopped a rogue starship of Earth's from killing a Thanatosian planet's entire population, thereby preventing an interstellar war, all Earth's officials care about is how much you know about their top-secret Depopulation Bomb.
- The Un-Reveal: While it's eventually revealed that the crew of the Jeremiah Obrian were accidentally infected with the Iron Helix weapon, which is why the ship would no longer accept their commands, it's never revealed what caused the ship to reroute itself to Calliope in the first place.
- Utopia: The backstory in the manual states that Earth has "solved its problems of disease and prejudice" by the time of the game.
- What Happened to the Mouse?: The opening cutscene shows that the Jeremiah Obrian was traveling with another Cerberus-class ship, the John Paul Jones, however, this other ship is never mentioned again after the opening cutscene.