Alas, Poor Villain: Some of the enemy Masters get rather sad exits that shows they weren't really that bad.
Shinji's Villainous Breakdown does a 180º turn when it's revealed that he's just a eight-year-old boy.
Alice is just a lost little girl who is already dead.
Rin/Rani go out commending you/silent and sad. Both have helped you quite a lot throughout the game, regardless of which route you took.
Julius comes back from the dead and shows you his life before trying one last time to kill you. Even the protagonist cries for him when seeing his life.
Leonard goes out with grace and finally has the perspective to realize not everyone thinks like he does and, moreover, is not necessarily wrong for thinking otherwise. He also shows he means it when he said he did not care about any personal benefits he may gain.
Alternate Timeline: Supposedly, this game takes place in a timeline that diverged from the normal Fate/stay night universe in 1980, when the prana of the world suddenly vanished. According to Rin and Twice, this shouldn't have happened, and history is corrupted somehow. Also, the moon landings haven't taken place yet, despite occurring in the normal timeline before the prana vanished. Leo's dialogue implies the Harway family prevented space-travel to prevent anyone from landing on the Moon.
And You Thought It Was a Game: Many of the Masters view the Holy Grail War as just an online game at first, and don't fully comprehend the consequences of losing. The results of the first round drive the point home to most of the surviving participants.
Angrish: The Berserker class Servants' incoherent speech due to Mad Enhancement.
Bittersweet Ending: You stop Twice's plans to create a Forever War and obtain the Holy Grail, but you are essentially erased in the process and your female partner is the only one to truly escape the Holy Grail War. She's looking for your real body, but it won't have any of your memories since you're just a copy of that person. And the real world is still stagnant and oppressed, but at the very least the Holy Grail War is no longer deadly and Twice can no longer use the Moon Cell to make things worse. Welcome to the Nasuverse!
In CCC Normal Ending, everything's back to normal that you finally returned to the Near Side from where you left off. But, you have no recollection of Sakura and the Far Side. While in the CCC Route Ending, You permanently lose your servant and BB sacrifices herself. Sakura ends up creating a new body for herself and the Protagonists. Jinako, Rani, and Rin are also implied to have survived as well since they were the remaining masters, but the events of Extra still continue even in the CCC Route, leaving it inevitable that either Rani or Rin will be dead in the end.
Blank Book: One of the clues in the prologue that shows that things are not right is the school's student registry being completely blank.
Bonus Boss: The original has Shiki Ryougi. CCC includes three more bosses of Rin Tohsaka and Alternate Playable Archer, Kotomine and Lancer, and Twice H. Pierceman and Playable Caster. All three appearing thanks to the Moon Cell.
Bonus Dungeon: The Zeroth/Infinite Chimeric Lunar Sea, accessible before you go to claim the Holy Grail. However, it's not that difficult and doesn't have anything of value except for the Bonus Boss, if you've unlocked her.
Book Ends: The beginning and the end of the Holy Grail War for the protagonists involves walking down a long corridor that changes shape as you move along it.
But Thou Must: Sometimes, you only get one dialogue option, like when Alice asks you to play with her and attempting to peek in on your Servant getting... 'recharged'.
Character Level: Your level as a Master increases when you gain enough XP after defeating enemy programs, which also has the effect of empowering your Servant. You also get 3 Skill Points per level, which you can use to boost your Servant's stats.
Twice H. Pieceman actually makes a early appearance during the 3rd week, which also comes with a Chekhov's Gun related to Alice and a plot point later in the game.
Why couldn't the Decoy Protagonist use a single attack with his Effigy? Because Julius had gotten his Servant before the Grail War started, according to his backstory, and he had Li Shu Wen shred the Decoy Protagonist's Magic Circuits. That's why Julius didn't kill him and just knocked him out. Without Magic Circuits, he was doomed anyway.
Color-Coded for Your Convenience: After the War begins, this is how you distinguish non-unique Master models from regular NPCs. They both wear the same yellow-brown school uniform, but in different shades. Masters wear the brighter ones from the prologue, NPCs wear a darker shade. Also, Student Council members wear black.
Decoy Protagonist: The initial playable character is a Master candidate who fails his trial. Once you get control of the "proper" player character, an interesting (and really creepy) perspective flip occurs on several events.
Deus Sex Machina: Rani or Rin has to use this to repair your Servant's Magic Circuits after Assassin destroys them. However, you're kicked out after you activate a trap that's meant to kill anyone who peeks. All you really see is a bare leg, but Sakura's dialogue after you look in and your Servant's dialogue later on even if you didn't practically confirms it.
Digital Avatar: Nearly everyone you meet in the Moon Cell. Whether they look the same in the real world is never mentioned.
Disappears into Light: Masters and Servants defeated in the Elimination Battles are covered in darkness and are deleted; Nursery Rhyme just vanishes to become someone new, Arcueid tears her way out, Ryougi vanishes, probably to another world, and Savior disappears into glowing light.
Epiphanic Prison: The game starts off in one; it takes the form of a very cliche school drama/comedy setting. Realizing that everything is fake and trying to assert your identity even when you can't remember it is apparently the preliminary section of the Holy Grail War. Only 128 people succeed, including the protagonist.
Sakura has one of the biggest bosoms in the Nasuverse, which is combined with rather unkempt hair, both of which were amplified here. Sakura's already well-sized breasts became even more noticeable, and her unkempt waist-length hair now goes down to her knees. Sakura basically took Medusa's measurements for herself, except for her height, hence her Fan Nickname Sakurider.
CCC introduces three seeming Sakura clones, one of which, named Passion Lip, is even bustier.
Rin's curves are more pronounced compared to her original design.
Fission Mailed: After you beat week two, the game deliberately makes you think you've entered a Bad End of some sort, straight down to subtitling it Dead End like one of the non-combat game overs you can get... and then your Servant and Rin barely save your life. (Rin didn't even mean to, hilariously enough. At least, that's what she says.)
The sentences that pop up on the bottom left of the screen showing off the Arena just before you enter it tend to be quite relevant to whoever it is you're fighting in that week.
A more comedic example is in the prologue. If you talk to one of the students outside, she says that "You'll have to pick sides in the nerd war soon." On the 3rd day of the 4th week, talking to the male student outside, whose opponent is a manga fan while he's a comic book fan, forces you to choose which one you're a fan of, or you could pick bande dessinee.
Early on in the War, you learn that there's a Master who's hanging out in the Chapel, complaining that she hasn't received a Servant yet due to a 'system malfunction'. You also learn that the reason for having only 128 participants is due to that being the maximum number of Servants the SE.RA.PH can support at once. So, there's one Servant unaccounted for... and it turns out to be the Final Boss.
Another early one, the dream sequence just after the beginning of the first week is of a disaster that claimed many lives. The way it's written implies that it's a memory of the original Twice's last moments before he dies during the terrorist attack.
There is a Master in the garden outside the chapel who's quite knowledgeable about flowers. The meanings of each of the flowers she mentions is very relevant to current events.
In one week, you see a transparent figure walk towards you before disappearing, and Leo explains that it was a digital ghost, that you shouldn't worry because they're just images that can't affect anything. The figure you see is Twice Pieceman, you are a digital ghost who's damn well affecting things, and after he's defeated, Twice walks towards and past you, fading away as he did in the hall.
For Want of a Nail: You could either save Rin or Rani from the other. This also changes which Master and Servant teams you fight later.
In Spite of a Nail: You still face the Harway brothers, Julius and Leonard, as the fifth and seventh Masters respectively.
The Information Matrix has four points on it; finding out enough about your opponent to fill them all gives you an advantage that comes in handy when you're fighting them.
Potential Masters had four days to realize they were being tested and prove their mettle; failing to question reality enough or survive the tests ended poorly for everyone who didn't qualify.
Plays a role in the first battle with Assassin. Every round, his fourth move is an auto-counter to your fourth move, unless you used a Skill.
Gender Flip: As before, a couple of Servants are female incarnations of male historical figures.
The Ghost: Rani's Professor, who is a member of the Eltnam family like Sion.
Grand Theft Me: Julius B. Harway took the place of Souichirou Kuzuki by hacking his profile.
Guide Dang It: Getting the playable Caster's Matrix Level to E relies on a series of specific conversation choices throughout the game, and most of these don't look like they're significant at all. Here is a very detailed guide.
Ham-to-Ham Combat: The playable Saber versus Dan Blackmore's Archer. Quite hilarious, and awesome, as they snark-off.
The Hedonist: Rider's personality. If you choose Saber, she also shows some of this, such as when she congratulates the protagonist on using 200 items for such overt consumption, and decides that she needs to keep up by upgrading one of her skills to do more damage, but consume more MP as well.
Hello, Insert Name Here: Naturally, you get to come up with the Protagonist's given name, surname, and nickname (which can naturally be the same as their given name). In voice, though, Saber calls you "Praetor", Archer calls you "Master", and Caster calls you "Goshujin-sama"; which can both mean "Master" and a respectful way of saying "Husband."
Twice H. Pieceman's Servant Saver has a condition where every two turns, a mirror lights up. If all seven mirrors are lit, you lose and he wins.
If a Master does not obtain the two Triggers in the Arena before the Elimination Battle at the end of the week, the other Master wins by default. This can happen to you, so don't slack off on Dungeon Crawling.
It's a Wonderful Failure: If you get a Bad End or lose in an Elimination Battle, the game describes what happens, and in the case of the Elimination Battles, your opponent has several things to say to you.
Luck-Based Mission: Due to how combat works, just trying to fight normal enemies can become one of these. It gets easier the more you fight the same enemy, but it's quite possible for a fragile character like Caster to be taken from full HP to dead if you're unlucky enough, particularly later on in the game.
More Dakka: Rider's Noble Phantasm, Hunt of the Golden Hind, fires a barrage of cannons from her armada. It is substantially more awesome than the simple description makes it sound.
Multiple Endings: In CCC. The Servant Endings require one to collect their Secret Gardens.
The normal ending has it All Just a Dream and it's stated the events of the first Fate/EXTRA game still continue(CCC takes place during it).
Gilgamesh Servant Ending. Gilgamesh appears and reveals that the Protagonists original servant was a Berserker and saves them from the Moon Cell by sacrificing 90% of his NP treasury and defying the Moon Cell in the process. He then takes them to a alien world 1500 lightyears away. With the two planning on exploring this new alien world.
Archer Servant Ending. The Protagonist appears mysteriously on earth and meet a mysterious man who looks like Archer. Wanted by the Harways, they then have the mysterious man become their battle instructor.
Saber Servant Ending. Saber saves the Protagonist from certain death and uses Aestus Domus Aurea to create a Church, where the two get married at.
Caster Servant Ending. Caster saves the Protagonist by using the Moon Cell to summoner her other 8 Tails as Servants. With the Nine working together to save them.
CCC Route Ending. Beating the normal ending for CCC, completing Extra's story again, and then starting a New Game+ of CCC afterwards will give one access to the CCC Route and ending. There are also other requirements throughout the story that must be done through the game to face the True Final Boss and ending.
New Game+: You get to carry over your Arena enemy combat data, money, your Formal Wear (aside from Servant specific ones and one unlocked through plot progression), and it lets you skip the prologue to the point when you select your Servant. You also get a chance to fight the Bonus Boss.
N.G.O. Superpower: The Harway family owns 30% of the real world's land and 60% of its wealth. They even have their own army.
No Fair Cheating: In-Universe example: attacking your designated opponent on school grounds will result in a penalty to your Servant's stats and fighting in the Arena before the Elimination Battle is limited to three rounds before the system breaks up the fight. Often, this helps you more than it hinders, as it pulls you out of most Hopeless Boss Fights.
The prologue uniquely has YOU as one of the many nameless, identity-less faces wandering around the school. The guy realizes to his horror that, like the protagonists of Rosencrantz and Guildenstern Are Dead, he has no memories at all of how he got there, what he's supposed to be doing, where he's going or even if he exists at all as a person.
Played straight in a less-meta sense: don't expect to fight anyone who doesn't have a character portrait, or a name.
Non-Standard Game Over: It's possible to get a number of Bad Ends in the game, including one if you go the wrong direction in the prologue. Granted, you really have to ignore the game prodding you away in order to get that one.
Rainbow Speak: Blue is generally used for characters, like your Servant and the other Masters. Red is usually used for important terms and for enemy Servants. Gold is only used once, in a book you can read if you visit the library during the 4th week.
Saber is easy (just don't miss any of the conversations marked with yellow) and Archer is only slightly harder (same as Saber, but you have to ask about his true name in the 7th week). Caster is the most difficult: in addition to the yellow conversations, she gives you a survey in the 4th week and the wrong answers will make it impossible to maximise her Matrix Level. You also lock her "Extra" level if you dodge her question about who you love in the 6th Week (even if it's not her).
The values carry over to CCC.
Red Herring: During the early part of the 6th week, it's heavily implied that Leo is your opponent. It's actually the girl you didn't save.
Shaggy Dog Story: Your quest to survive ends in failure and your goal of attempting to stop Leo and Julius was pointless. Twice would have killed anyone else who made it to him apart from maybe Tohsaka due to their similar ideas, but almost certainly not even her. You do manage to stop Twice himself, but you had no idea he was there, no idea he was making things worse on Earth and your character not only has no attachment to Earth but also cannot really be 'revived' thanks to a lack of medical knowledge.
Just before having to choose whether to save Rani or Rin, look at the middle row of the code that pops up when the protagonist touches the film projector. You can see the numbers 999 and the words BlazBLUE and AGAreST, all of which were also translated by Aksys Games.
There's mention of a book about sparkly vampires if you look at one of the shelves in the library.
In Fate/Extra CCC, Caster revealing her enormous goddess form is almost identical to the protagonist meeting Gwynevere.
Small Name, Big Ego: Shinji spends most of his time shrieking and whining about how he's better than everyone else, but we don't really see much justification for this other than his apparently-good coding skills. This is, of course, perfectly normal behavior for someone who is only eight years old.
Something about a Rose: The playable Saber has rose petals appear in some of her special skills and when she summons her Noble Phantasm.
Standard Status Effect: Poison/Curse/Sacrifice (standard damage inflicted per turn), Paralysis/Stun (prevents being able to act on random moves on a turn, Stun only lasts for one turn) and Seal (prevents the afflicted from using the move that is sealed). Typically inflicted by Skills, though some of the later enemy programs and Servants have a small chance of inflicting them using normal moves.
There Can Be Only One: Even more so than the original universe; killing the Servant kills the Master as well (except in very special circumstances, like in the Rin vs Rani battle). Also, only 1 out of 128 Masters may claim the Holy Grail, and even more had died in the prelims. The winner also has to beat Twice H. Pieceman, because he still counts as a Master, and only when there is one Master left do they get to leave.
Trial-and-Error Gameplay: Combined with Tactical Rock-Paper-Scissors above. You select six moves per turn, and the enemy does the same thing... but you might only know one or even none of the enemy's moves in advance. Eventually, you'll figure out the patterns (and, helpfully, monster families all behave in a similar manner, so later in the game you won't be totally helpless if you've been paying attention), but usually not before dying a few times.
And, in case this isn't enough, defeating enemy programs enough times allows you to uncover more of their moves on the move queue, so eventually there will be less guesswork. This carries over in a New Game+, which is handy.
With Servants, you have to gain information on them. The higher your Matrix Level, the more of their moves are revealed. This is not carried over in a New Game+, but if you managed to do it the first time, you should be able to do it again. Also, when you fight against them in the Arena, the patterns they use then will still be used in the Elimination Battle.
For enemies like the Bonus Boss, whom you have no way of gathering info on or memorizing their pattens beforehand, three of their actions are revealed per turn.
Tron Lines: Pretty much everything in the Arena have them - the walls, the monsters, the treasures, etc. Even the playable Saber's sword gives off the appearance. Rin's Lancer-class Servant has quite a few as well.
The Unfought: Even though there are 128 Masters, you only get to fight 7 of them, each using different Servant classes (which results in you fighting one Servant of each class in the end).
Justified since it's a knockout tournament, so most of them are beaten by other Masters first, and considering that the losers die...
There's also the fact that Shiki Ryougi killed 99 Servants (and their Masters by proxy), possibly during the prelims as well, since there was mention of a spate of murders going on in the prologue.
The transition of the prologue seems to indicate that before the preliminaries ended, there were at least 999 Master candidates participating, most of whom never even made it to their first battle.
Visual Novel: It's more of a RPG with a novel battle system, but it retains the Visual Novel roots of the Fate/ series by having lots of screens of first-person narration as well as Bad Ends.
Win to Exit: The only way to leave the Holy Grail War is to be the last Master standing. This includes Twice H. Pieceman and the Servantless girl you saved. Once the protagonist beats Twice, claims the Holy Grail and gets deleted in the process, the girl s/he saved leaves, and swears to find the protagonist's real body.
Writers Cannot Do Math: The bonus boss has killed 99 Servant pairs. You have beaten seven Masters by this point, all of whom killed their own opponents up to that point as well. Indeed, Julius killed many more than that. This adds up to a total well above the 128 Servant limit stated in the game.
You All Look Familiar: Justified, due to Digital Avatar. Most of the Masters in the War use the default avatars, which are shared with the NPCs, while the skilled ones like Rin and Leo can customize theirs. The protagonists are in-between, they have unique faces, but wear the default clothing. This is because they're a NPC based on a real person.
Archer mentions in a Private Room conversation that an Avatar's appearance is related to the person's capability for magic. Those with tremendous capability, like Rin and Leo, retain nearly all of their physical body and reject the default school uniform. Those who have low capability are stuck using the defaults. Those in the middle, like Shinji and the protagonist, keep their basic physical appearance, but are stuck using the uniform.
Though it could be argued that Shinji choose to keep the uniform as to play out the role of 'Shinji'.