Big Bad: Councillor Dule and the Centurian Collective.
The Kalaxian cult. Notable members include Noir, who is the first person to defeat the Captain in combat.
Black Comedy: First, choose a random item in the game. Then, scroll over it. Now, read the flavor text. There's a one in ten chance it won't be a case of this.
Blood Knight: Holy crap, Ragnar'. It's one of the reasons why he joins up.
Boss Battle: At the end of each stage. Also, raids, which are boss battles involving multiple players and a time limit.
Bribing Your Way to Victory: Par for the course, but downplayed, you accumulate Golden Suns, the game's premium content currency over the course of gameplay, rather than just by shelling out real money (way more slowly than Credits, of course), and if the Random Number Generator is favourable, you can get certain outfits by hammering away at certain high-level raids and hope they drop a Facility plan, and some really good items as part of the Gift-per-Day.
Bunny-Ears Lawyer: One party member is an expert markswoman, who calls herself "Vulpina," who insists on wearing a cat costume. Her flavor text:
"When someone wearing a furry costume asked to join your ranks, your first impulse was to give her a good hard slap and send her on her way. Then she pulled out her laser pistol and shot the wings off a nearby fly. So you allowed her to join, on the condition she remove the mask portion of her costume. You refuse to hold a conversation with the face of a cartoonish feline."
Cool Ship: You can buy and obtain some and man them with your officers and crew.
Darker and Edgier: Starts with Illaria's death and gets worse from there. Your character is psychologically damaged, and attempts to commit suicide. Eventually, you become a burning engine of vengeance, to the point where you don't think twice about committing planetary genocide.
And then your main character leaves the party.
Death Is a Slap on the Wrist: Dying doesn't really affect gameplay. All you need to do is spend some credits on health, and you'll be able to participate in PVP fights and boss battles again.
Difficulty Spike: Noted especially from going from Zone 7 to Zone 8, where bosses suddenly do significantly more damage.
Going to Hard difficulty in most post-8 Zones; while patches have limited requirements for Normal missions to relatively easy-to-get items, the requirements remain unchanged from when they were first released in the tougher difficulties. Among other things, one particular section in Zone 9 requires the Dragon Cycle, an item whose parts require attacking specific raid bosses with specific items equipped - one requiring you to complete a certain section in Nightmare difficulty, just for a single officer.
Evil Plan: Councillor Dule of the Centurian Collective. He gets the crew to attempt a rescue attempt on the held-captive Sian Emperor, deep in enemy-occupied territory. He allows the player to succeed in this rescue mission, providing sufficient resistance to avoid suspicion. Once the Sian Emperor has been rescued, his body, under the control of the collective, kills Illaria.
Tragically, it fails to be a Xanatos Gambit by a crucial issue. He assumed this would weaken the heroes. Instead, it drives the Main Character to destroy the Collective, and personally kill Dule.
Experience Points: Obtained by doing missions, participating in raids, and fighting other players.
Exploding Barrels: Lampshaded during Zone 6, when you take advantage of red barrels. Princess Illaria even questions why anyone would leave such a dangerous object out in the open.
Expy: Princess Illaria is basically Princess Leia with a new hairstyle.
Sixth Ranger: Lu Bu is the last to join your main crew in the story, Rautha once he changes sides
Gone Horribly Right: The flavour text for the Lesser Unbreakable Injection item. a schoolyard bully forced his victim to take one so he wouldn't bruise, and got his ass handed to him because his punches couldn't hurt the other kid.
Gotta Catch 'Em All: The collections, for starters. To be able to obtain components for rarer items, and to complete Zone 9 items, you'll need a variety of different items. Time to start collecting!
Heel-Face Turn: Rautha. After you fight him numerous times, including once when he comes at you nothing more than a head in a jar attached to a robotic body, you take his head with you to prevent further encounters with him. His allies couldn't care less, much to Rautha's upset. Over the next little while, Illaria has been kind to him, despite all of his previous attempts to kill her and the rest of your crew. Then, when Illaria is killed by the Centurian Collective's plan, Rautha swears revenge on the collective, and joins your crew as an Officer.
Horny Vikings: The Niflungs are essentially this in space. No horned helmets, but they do have space chain mail.
Impossible Thief: Lupin. He once stole a necklace Illaria was wearing and replaced it with a fake without her noticing.
Lost Forever: Many limited-time items can only be purchased in a small timeframe, although some do reappear after a while (but not all of them).
Luck-Based Mission: The raids. When a raid boss is defeated, you can usually obtain up to 9 random items. Some of these items are required for obtaining components for rarer items, and completing Zone 9 missions.
Here There Were Dragons: The humans come from Tor'gyll, a place where magic very much exists, of, and the player character descended from the great Dragon rider of West Kruna, yes, he rode a dragon, and it talked and it spoke to the first emperor of the Sian empire. However, for unexplained reasons the magic has since disappeared. It is implied the Psychics are the only practitioners of magic left.
Money for Nothing: There are only three ways to spend credits after recent patches made Facilities free - to restore health, to use in the shop (probably for raid summoners), and as payment if you lose in PvP. That said, the money you use in the latter two are so small as to be insignificant, and certain powerleveling builds can allow a player to level up (with free refills) without needing to spend any credits.
Mooks: Most notably, the Centurian Collective soldiers. Several Contella Enforcers have been referred to as mooks as well.
Retired Monster: YOU! The Captain becomes this, after leaving the party. Essentially s/he just wants to be left alone, having nothing left.
Turns Red: All raid bosses start out with their default artwork. Once they take enough damage, the artwork changes, depicting the battle as it rages on. Starting from Zone 7, this also applies to mission bosses.