Aquanox

Basically, an underwater vehicular combat sim, created by now defunct German developer Massive Development (not to be confused with Swedish studio Massive Entertainment). The game is a direct sequel to their earlier title Archimedean Dynasty (a.k.a. Silent Running, which takes place in the same fictional universe a few years prior.

In the future, due to World War Three and an antimatter meteorite, civilisation will be forced to emigrate and live in underwater stations in the depth of the ocean.

In the first game, you are Emerald "Deadeye" Flint, a mercenary fighting a race of cyborgs called the Bionts (picking up from where you left off in Archimedean Dynasty).

In the second game (whose events happen simultaneously with those of the first) you play as William Drake, a young (and initially quite naive) man whose cargo freighter gets hijacked by a bunch of pirates, led by a treasure-obsessed man named Amitab, who then shanghai him into fighting for them. It Gets Worse.

This game series contains examples of :
"Sally: Get your butt to navigation point one!"
 * After the End
 * And Now for Someone Completely Different : The switch from Flint to Will Drake in the last game of the trilogy.
 * Apocalypse How: Class 1.
 * Ars Goetia: The namesakes of the Old Ones.
 * Awesome but Impractical: The Vendetta Sniper gun can be used to shoot through people's cockpits for an instant kill when it's zoomed in... but it does very little damage if it hits anywhere else, has a long reload cycle, and cockpits can be REALLY hard to hit on a moving vehicle, especially when you're being shot at and have to stay in motion yourself.
 * Awesome McCoolname: Emerald "Deadeye" Flint.
 * Battle Royale With Cheese: The battle for Neopolis, which features lots of characters from throughout the game.
 * The Battlestar: Aquanox has two unique super-carriers, the Crawler's Magma Eater and Iwan King's Creole Girl.
 * Beam Spam: Gatling Laser, Gatling Plasma.
 * Big Bad Duumvirate: Aquanox has rogue Federation military commander Commodore Sool and the Crawler leader Samuel Korhonen. Sool is a crypto-fascist who wants to take over the Federation and reclaim the surface, while Korhonen is a megalomaniacal madman who basically wants to eat everyone. Although they're working together, each plans to eliminate the other once the Federation and Flint have been dealt with.
 * Continuity Nod: Done repeatedly throughout Aquanox, which keeps referring to the events of Archimedean Dynasty, and also through Aquanox 2, which refers to events of Aquanox and its prequel.
 * Cool Sub: ...and how!
 * Corrupt Corporate Executive: Vanderwaal used to be this, until he lost control of EnTrOx.
 * Crowning Moment of Funny: When Forneus sneaks behind and eats Cohonen.
 * Cyberpunk / Bio Punk / Playing With Syringes : Oodles of it.
 * Darker and Edgier: When compared to Archimedean Dynasty (which was already pretty gritty to begin with).
 * Dystopia: Though mostly prosperous and highly technologically advanced, the society of Aqua is also extremely corrupt and decadent.
 * Dummied Out: Originally, one mission would have pitted Flint against a liopleurodon; The sound files for the mission are still present. In the actual game a character even gives him a tip on how to defeat one, should he ever encounter one.
 * Eldritch Abomination: The Squids, Forneus, all Bionts, Drake's Creature (the plot isn't really clear if it's some sort of Squid or something completely seperate).
 * Enemy Mine: Aquanox's finale has the Atlantic Federation, Entrox Corporation, Tornado Zone pirates, and even the Bionts all joining forces against the Crawlers and the Squids. Flint remarks that joining forces with the Bionts is an incredible Idiot Ball move.
 * Escort Mission: An alarming number of them, although most are tolerable once you figure out what you're supposed to do.
 * Eviler Than Thou: The Squids pull this on all the other villain factions when they show up in Aquanox's final act. The Bionts end up pulling one on the Squids in the game's ending.
 * Fallen Hero: Admiral Cox becomes an antagonist and leads a coup. He gets an Alas Poor Villain.
 * Forbidden Zone: The surface world, "where the pressure is so low that explosive decompression is inevitable." Besides a few idealists and cultists, no one gives any serious thought to trying to recolonize the landmasses of Earth, even though it's been centuries since the wars and successive disasters that ruined it.
 * Gainax Ending: Aquanox and Aquanox II both feature end cutscenes with a lot of exposition and very little explanation, and suggestions of a possible future story or sequel that has not materialized.
 * Gatling Good: Vendetta Gatling, among others. See Beam Spam.
 * Game Breaking Bug: The last level of Aquanox is broken and often renders the game Unwinnable, due to the final boss failing to appear at the end of the mission. This is mostly caused by installing the final 1.7 patch instead of the earlier 1.5 patch, but sometimes happens even with the 1.5 version of the game.
 * Genetic Engineering Is the New Nuke : The biont monsters.
 * Hot Sub On Sub Action: Obviously.
 * Humans Are Bastards: Even the apparent good guys of Aqua are morally ambiguous at best.
 * Human Resources: The Crawlers are cannibals, and it's revealed that the Bionts capture humans and break them down into base proteins to fuel their bio-organic parts.
 * Kill Sat: Project Brainfire.
 * Landmarking the Hidden Base: At one point, you attack a base centered around the Statue of Liberty.
 * Loads and Loads of Characters: Flint has an enormous amount of "old friends", and a lot of them return in Aquanox II.
 * Lost Superweapon / Ancient Artifact Of Doom: The Federation's Brainfire Project turns out to be an attempt to gain control of one of the remaining pre-war orbital satellite lasers.
 * Lowered Monster Difficulty: The Bionts, the Big Bad faction of Archimedean Dynasty, have been reduced to a weak group of Remnants who serve as the enemies in the game's first Act. Their ships are noticeably weaker and slower than they were in Archimedean Dynasty; justified in that the remaining Bionts in Aqua are stray units leftover from the destruction of their civilization in the first game, who have not been maintained or repaired for more than a year.
 * Macross Missile Massacre: The Hydra gun essentially spews out a continuous stream of small, short-ranged, lightweight, target-seeking torpedoes.
 * Most Annoying Sound:


 * Outside Context Villain: The Squids serve this role in Aquanox, similar to the Bionts in Archimedean Dynasty.
 * Pinball Protagonist: William Drake doesn't really take the initiative to choose his own course or even ask hard questions about the course of others. Whenever he does make any decisions on his own, they are nearly always ill-informed.
 * Police Are Useless: Yup. Aqua is more or less lawless outside of the habitats, and known murderers are often seen walking around inside those habitats without any problems. The police subs that patrol the areas around the habs are often mysteriously not present so that Flint can take jobs that they are supposed to do, and they die by the sub-load whenever you take a mission that pits you against them. On the rare occasions where they are present and supporting you, they still won't actually do very much.
 * Protagonist Centered Morality: Neither Flint nor Drake seem overly troubled by the huge numbers of people they kill, no matter who they are, and no one ever takes them to task for it either. Occasionally, someone will voice a sentence of complaint, but it never becomes a part of the plot.
 * Sea Mine: There are levels dedicated to these. Worst of all are levels where you must do an Escort Mission for a ship that is incapable of doing its own minesweeping.
 * Silly Rabbit Idealism Is for Kids: Flint and co. do good work for better credits.
 * Amitab's pirate crew give speeches about this trope to Drake whenever he complains about their actions, or their continual abuse of him.
 * Submarine Girl: Sally is both this and the Computer Voice of Flint's sub.
 * Sub Story: A futuristic take on it.
 * The End of the World As We Know It: The surface has been rendered uninhabitable and the oceans are covered with an impenetrable layer of highly radioactive dead organic matter which makes travel to the surface impossible. What's left of mankind lives purely Under the Sea.
 * The Stoic / Deadpan Snarker: Flint (in contrast to Archimedean Dynasty, where he was more of a cheerful Loveable Rogue).
 * Title Drop: In the first game, one conversation with a rather philosophical person will have him refer to the bad state of the world as "Aquanox, the watery night".
 * Travelling At the Speed of Plot: The "dipole drive" serves like the underwater equivalent of a hyperdrive, teleporting enemies away and out of reach when they need to leave the stage, or yourself at the end of a mission. You can't actually use it during the mission, even if you want to hurry up.
 * Truce Zone: Combat inside of habitats is apparently strickly taboo, and various thugs and rivals will often meet you inside of bars to trash talk you, before the two of you head outside to your subs to fight it out. At one point towards the end of the first game, you can find the two most wanted men on the planet (pretty much the setting's equivalents of Hitler and Osama Bin Laden) strolling casually around in a city park waiting to talk to you.
 * The Unfought: You never actually fight a proper duel against Big Bad Samuel Korhonen or his Ace Custom sub; although he participates in some of the end-game firefights, he warps away after a very short period of time. At the end he gets eaten by the final boss in a cutscene.
 * Unwinnable: In one version of the game, the final part of the final mission is bugged.
 * Used Future: An underwater version - but a lot of the subs still look really awesome.
 * The Usual Adversaries: The Crawlers, a deep-dwelling civilization of cannibals hostile towards all of the other human civilizations.
 * Water does not work that way: Critically damaged ships suffer explosive decompression, which would make sense in space... Except that under miles of ocean, they should implode instead.
 * The Wall Around the World: A highly radioactive layer of dead organic matter completely covers the oceans near the surface, preventing any attempts to travel to the surface world.
 * Western Terrorists: One of the problems facing the world of Aqua are "Terror Tourists", bored Federation youths who travel to poorer non-Federation areas and randomly blow up habitats and property for giggles.
 * What Could Have Been: Aquanox and Aquanox II start and end in the same in-universe timeframe, each with a rather large cliffhanger promising more epic adventures No sequel was ever made.
 * Wide Eyed Idealist: William Drake, at first. He gets better in this regard.
 * Would Not Shoot a Good Guy: Admiral Cox's rebel forces primarily fight with non-lethal EMP weaponry, which disable enemy subs instead of destroying them. The player is encouraged to return the favor, but there's no real gameplay or plot punishment for just straight killing them instead.
 * Yandere: May Ling, AKA "MayDay".
 * X Meets Y : Crimson Skies meets a Darker and Edgier version of Sea Quest DSV.