Here. Congratulations! You've been displaced from your home dimension by a sapient spaceship named Stacy, and now you and the rest of the crew have to save the multiverse from an alien menace called the Ohm. Have fun!
This game provides examples of:
Absence Makes the Heart Go Yonder: Averted. Many couples have gone separate for a great deal of the game and have recently been reunited, in particular Will Vandom and Matt Olsen as Will had been part of the crew for the longest time and Matt only showing up as early as December.
This is now played straight with a number of characters.
A number of monogamous characters still hold out for their loved ones. Goliath is still pining for Elisa, Sokka is still pining for Suki, Dr. Sam for his wife, Kang for his mate Fonrar...
Aliens Are Bastards: So far, just about every race the crew meets are either complete and utter bastards who don't give a rat's ass about what the crew thinks (such as the Galileians, who branded the crew's clones and stole everyone's DNA) or want them to pretty much submit and just be their personal playthings (like the Daligig are proving to be).
Anyone Can Die: B5 is destroyed in saving the ship from pirates, Kawalsky dies when Jonas/Vision crushes the parasite in his brain, and Superman perishes in a Heroic Sacrifice to save Lirath.
Apocalypse How: It's assumed that the Ohm have caused at least a Class X-5 (Multiversal Destruction) and are heading for Class Z (Destruction of Reality).
Artificial Intelligence: Several. Stacy herself is on charge of the entire ship, while AIs such as Cortana, GLaDOS, and Tex, and a couple of original AI characters run various aspects of the ship's day-to-day life.
Burial in Space: The mass of people-turned-zombies and Brainiac 5 who were killed during the Big Reveal plot. The people whose remains were recovered after the Mole plot, Kawalsky and Private Hudson. Also, Superman. Given the tone and plot of the game, they won't be the last, either.
Can't Have Sex, Ever: Before the Big Reveal, Stacy would not let anyone have sex. After the Reveal and Stacy's true AI returning, Stacy has allowed them to have sex, but only after a contraceptive shot is administered and only if they keep it to the crew quarters.
And a few people are still unlucky this way. Poor Steve.
Captain Ersatz: Because of the nature of the game, the Happy Happy Fun World planet is filled with knockoffs. Videogame Land takes this to a major extreme using Sonmari (an infamous NES Mario-in-Sonic 1 hack) and Sonichu'. It's also averted by the appearance of Princess Lara and Captain N himself.
Disaster Democracy: Took 'em two years OOCly, but they're getting around to it, finally. It caused a lot of bickering ICly due to the fact that some wanted a democracy and some wanted a militaristic government.
Enemy Mine: In theory, everyone. In practice... well.
Fake Memories: Kaya and Sasami are affected this way. For Kaya, it's revealed that she isn't Katara and that Katara's memories were given to her by Stacy by mistake, which gives the G Aang plenty of Aangst. For Sasami, it's revealed that her memories were tampered with and she's actually the one from the OVAs, not Tenchi Universe
Family Twists Index: Due to some timeline mishaps, this game features Mara You Are My Wife, Tycho You Are My Husband, Luke I Have Adopted You As My Father, Leia You Are My Sister, Vader You Are My Father.
Felony Misdemeanor: Ben Tennyson plays a prank that causes the crew to age or de-age thanks to Negi's age candy. Miku, Jaime, and Billy treat the prank as something akin to the Shiva incident
Five-Bad Band: The Strike Team. Essentially the ship's secret police, given authority to do what needs doing, no matter the methods or who they do it to.
The Dragon: Tenaya- She's very versatile, and will be sent on almost every mission.
The Evil Genius: Mei-Xing- She is a mage that relies on spell formulae, and has spent years studying magic, history, mechanical engineering, and architecture, among other things, to make her burglary jobs easier.
The Brute: Ronon Dex- A very brutal and skilled fighter, he's bound to show his face in any combat mission, despite being an unmodified human.
Failed a Spot Check: Marco says this to Kang after the later realizes he was the dog going around at the Lensmen's feet.
Fish Out of Temporal Water: There are plenty of moments here, especially with those in the past learning about their future. Scarlet Witch is shocked that she goes insane and even more shocked to learn Wolverine is part of the Avengers, Spider-Man's shocked to learn Captain America is dead, Lowe isn't thrilled over another war starting and Sasami's surprised to learn of other Kamen Rider series and has no clue who Hannah Montana is!
Gladiator Games: Zouichi, Anwei and Howard's mission on Epicurea ended up like this. They were not pleased.
Guns in Church: Before the zombie invasion, the Vatican was used to hold weapons there.
He Is Not My Boyfriend: Though toyed with by many characters, Lash takes this as far as it can go by dragging herself out of Medbay while seriously injured to rescue Zetta from space, yelling this trope at everyone in so many words as she goes.
Heroic BSOD: Damn near everyone after Warden!Stacy delivers the first Punishment towards Big Zero. Even Stacy suffers one.
Infinite Supplies / Unlimited Wardrobe: Averted - Despite two restaurant establishments (Kang's Drunken Dragon and Sasami's First Tree Cafe) and a clothing store (Rein Zwei's Stormwind Clothers), normal food is in short supply and there's usually enough material for at least one set of clothing for each crew member. The site's wiki has even gone so far as to point that out.
Interrupted Cooldown Hug: Kaya-Katara is able to start bringing Aang back to normal from his Avatar State after he was released. A few moments after it, Grif shoots him.
I Forgot I Could Fly: When Tyrant!Steve attacks Irma and a Kamen Rider Double formed Devlin Leven, Irma ends up realizing she never gave back her power upgrade Matt gave her way back during the Ohm attack.
Kick The Bitch: Considering how much of a major jerkass Big Zero is both in-canon and on the ship her receiving the Punishment and eventual death may count as this for Stacy and Nathaniel Richards respectively.
on the Taken page with (deceased) next to their name.
Locked Out of the Loop: Despite being rescued by the Daligig and being told to save the Multiverse, the crew still knows squat about what's going on, and it pisses them off when they find one of Stacy's little secrets. After Lirath, though, it seems the GIA is willing to help them out. Don't count on the Daligig, though.
Mad Scientist: Half of the Engineering and Science Departments probably qualify. One in particular, Wyn Callahan, cheerfully admits to being a mad scientist when asked, and probably has a touch of Science-Related Memetic Disorder to boot.
Lash literally gets to play this to all its cheesy, B-movie glory on a brainwashing plot.
MacGyvering: Under pressure, Howard's picked locks with a deconstructed spiral notebook and bic pen, powered a ventilator with a remote-controlled car, and made a dolly out of coke bottles, twine and plywood. Sometimes falls into Improvised Weapon, such as when he used a lighting cable to electrocute a robot jackal.
Mama Bear: When Vivio is struck down by an Ohm, what does Nanoha do? Unison with Reinforce Zwei and ramp it up to Blaster 3. Fate joins in with Shin Sonic Form, but doesn't Unison until a bit later.
Eva fits this trope as well, having hit Big Zero in the nose with her omnicomm over an altercation between Zero and Marco, and later having slammed a hardcover book into Iniss' face over his infesting Tom.
No Big Deal: The ship prevents characters from thinking much in detail about characters who have been "borrowed" by GLaDOS (player on hiatus) or returned to their pod (character no longer played).
And now, it REALLY gets wacky for its reasoning GLaDOS is checking those pulled away for "avia", essentially their souls, and if something isn't right, they're shoved back into their pods to save them. Needless to say, a lot of people are not too happy.
Noble Demon: Pretty much anyone who was or still claims to be evil is willing to play nice aboard the ship.
Not that they have much of a choice, mind you...!
Odd Friendship: Kanoe Zouichi and Howard Bassem. One's a self-sacrificing, heroic zombie-killer, and the other's a self-centered, amoral criminal. Somehow they still have a tight bond.
Ontological Mystery: Too many to count, although some answers were given. What happened to the previous crew? Is Stacy as benevolent as she seems? Are the Daligig trustworthy?
Orcus on His Throne: On the one hand, the Ohm are so busy with offstage villainy they rarely appear in the game. On the other, Lord Zetta temporarily regained his body and thus full access to the strongest mana power in the cosmos, but elected to spend his time playing video games and driving cool cars around.
Properly Paranoid: Many characters gain this attitude about Stacy, the original crew, and/or the Daligig after being there for a while. The ship itself stores or has at one time stored legions of battle droids, Reavers, homicidal AIs, etc etc.
Rocks Fall, Everyone Dies: According to one of the Daligig, the original crew of the Transmigration 9 (the player characters from the original incarnation) were either repodded or killed when they attempted to mutiny.
Romantic Two-Girl Friendship: Despite the presence of many Nanoha characters, the crew members most exemplifying the trope at present are... Hit Girl and Ruffnut.
Saving Christmas: A holiday plot had the characters awakening a spirit of generosity and goodwill that had been sealed away by a Mega Corp..
Translator Microbes: The crew, regardless of language or species, is able to understand one another through a ship-based translating system, which also happens to work while on different planets. Can be overridden by some natural foreign phrases and undisclosed curses. Subverted by Nehaalista, who gets away with sign language not everyone understands.
Trauma-Induced Amnesia: Thanks to the injury caused by the Ohm, Vivio has no recollection of anything from the impact to her wake up sometime after the fight.
Trecherous Spirit Chase: During the Nightmare King's initial assaults, he fools the crew with visions of their friends, loved ones or, in one case, worst nightmares.
The Handler: Kang is acting as both this and The Spymaster, at least until he finds someone else he trusts to do it.
The Spymaster: Kang, currently, also until he finds a trustworthy candidate to assist him.
The Virus: A rage virus intended for the Ohm accidentally infects the crew, causing them to turn on each other.
Later, Kawalsky was revealed to be infected with a creature known as Shiva, held Sheryl Nome hostage and was planning to detonate bombs unless the crew surrendered.
Aftermath of that? Cassandra Lang's killed by one of the bombs and Shiva and Kawalsky are killed by Jonas/Vision.
Not as major as the above ones but still very whammy, Katara, after many months on the ship was eventually repodded by Stacy. Come the next podpop she is initally confused as to why the hell she was put back only to remember that she was never Katara in the first place. Instead, she turned out to be Kaya, a girl who trained under Katara for a year. Stacy accidentally gave her her teacher's memories and Katara had really still been in podsleep all this time.
What Measure Is a Non-Human?: Oh, my God. Mei-Xing's clone was the center of a debate between Nanoha and the ship's Council. Mostly because they were afraid that if they agreed to let Mei-Xing have her clone back, it would be a blank check for everyone to claim their own clones as slaves!
You Are Grounded: Sherry convinces Vivio to sneak off for nighttime hi-jinx during SHORE LEAVE. Claire catches them and Leon and Nanoha are NOT PLEASED.