Who is June? A heroine justifiably seeking to save herself and give evildoers just desserts, or a villain willing to torture innocents and place them in fear of their lives to correct her own idiocy, possibly with an excessive taste for revenge? While Virtue's Last Reward keeps her moral ambiguity intact, most of Zero Time Dilemma heavily supports the former interpretation, going as far as showing that Akane's tendencies to plan murders in order to accomplish a noble goal only intensify in the ending that leads to Virtue's Last Reward.
Ace. Does he deserve any sympathy due to his cognitive disorder? Were his actions during the game a Machiavellian ploy devised by a sharp-minded sociopath or simply the result of a paranoia-ridden executive whose misdeeds came back to haunt him in a most frightening way?
Lotus. She mentions being fired from her cyber-security job and had twins who were abducted and forced to participate in the original Nonary game. How much do you want to bet she was fired for coming close to the truth? Throughout the game, she comes off as, alternatively, selfish and flightly (selfish when she points out that not everyone can live, and flighty when she tells you not to take her seriously), but she's probably using Obfuscating Stupidity. Unless you play the Torture Room, you'd have no idea she has hidden depths — when she talks about psychic powers, she always says it's "just a story." Unless you know she's connected to the first game, it makes no sense, but once you do, it becomes clear she's trying to give Junpei and the rest valuable information without tying it to herself. She's also one of the most competent puzzle-solvers when you work with her, suggesting that she's figured out more than she wants you to know. Badass. As for her noting that only so many of the players can survive to go through the doors? She never said she wasn't willing to sacrifice herself if necessary.
Junpei himself. Is he an ordinary guy trying to survive an impossible situation the best he can? Or a self-centered jackass willing to throw everyone else to the wolves to save himself and his loved ones?
Anti-Climax Boss: Not a boss in the strictest sense, but for all the hyping up the last puzzle got, that was one easy Sudoku.
Anvilicious: Not obvious at first, but after the game's ending, there is a clear theme running through this entire game: Do not judge things based on your immediate perception. Almost every single thing in this game is devoted to this theme, from the premise and ending down to tiny details such as how you perceive characters and how the puzzles are designed. This whole game is designed to subvert your expectations, and it WILL succeed, spoilers or not. This makes it clear that the developers really wanted people to be able to see things from multiple points of view, and refraining from judgment until you know the facts.
Complete Monster: Gentarou Hongou, better known by his code name "Ace", first appears as a helpful and altruistic ally. This all changes after he is revealed to be the CEO of Cradle Pharmaceutical and the game's true Big Bad. He created the First Nonary Game, kidnapping eighteen children and forcing them to commit numerous tasks with their lives on the line, for the sake ofcuring his prosopagnosia (inability to recognize faces). He personally shoves the young Akane in an incinerator after an unsuccessful escape attempt where she burns alive, being too frightened and clueless to solve the sudoku puzzle required to escape. In the Second Nonary Game, this time as a participant himself, he intends to betray and murder everyone in exchange for their bracelets, succeeding in the Submarine Ending. First, he successfully murders his three colleagues in order to hide his identity and keep his crimes from never reaching the court. He also murders Clover in the alternate Safe Ending, later taunting her brother Snake how he loved the sensation. An utterly corrupted, delusional and sadistic man, he is willing to murder anyone who stands in his way while at the same time trying to claim that he is a tragic individual.
Snake. According to a poll by Aksys he's the most popular character in the game in the US.
Polls show that Clover's the most popular character in the game in Japan, and is second only to her brother in the US.
Esoteric Happy Ending: The upbeat "love conquers all" vibe becomes Fridge Horror when you realize main character Junpei is unable to stop loving the person who effectively tortured innocents to survive and murdered those who wronged her, and who leaves him without a word. In the Virtue's Last Reward timeline, he even becomes disillusioned after unsuccessfully chasing her for the rest of his life. However, the Golden Ending of Zero Time Dilemma ultimately subverts this, as Akane is given a much more sympathetic characterization, and her and Junpei end up forming a close relationship, both professionally and personally. And to be fair, you can consider Akane's actions an extremely bizarre form of murder in self-defense. Young Akane needed someone to connect with in the exact same situation. Junpei or Santa wasn't just going to stumble into a Nonary Game. The only future she found where Junpei was in the same proper frame of mind was one where she put him there. Word of God confirms that Junpei would have been willing to save a girl's life had he been asked, just the situation kind of forced it to be involuntary. And deaths surely helped Junpei be in the proper Nonary Game setting to connect with. Considering that these bastards are going to kill Young Akane if she doesn't kidnap them 9 years later and thus save herself.... Also, look at what Junpei does to ensure he enters Door #3 if he insists on taking that path. He certainly understands being a Magnificent Bastard to get what you want, and thus is less likely to hold Akane's actions against her, especially considering she had a much more understandable reason for her actions (read: escaping imminent death and exacting vengeance on the ones who put her through hell) than Junpei did (read: possibly condemning three apparently innocent people to death because he wanted to stay with June).
Fan-Preferred Couple: Snake/Santa is a rather popular pairing, it's very helpful that the former is implied to be gay and the latter has been confirmed to be bisexual.
June's story of the rabbit hutches predicted the deaths of the players, except Ace in Submarine ending, in which they were the rabbits while Junpei is responsible for catching the killer.
In the True ending, Ace explained that he only found a mandrake root inside the coffin. In Greek mythology, Mandrake root symbolizes immortality and whoever eats that plant, they went to sleep and never woke up. Other folklore claims that mandrake root links sexual behavior or as a worship to the devil.
Hermes, the Greek god on whom Mercury is based, is a messenger of gods and he often guides travelers to go on safe journey. He's also served as a trickster that's why many Greeks wanted to sacrifice for him. In the Ax and Submarine endings, the mercury symbol at the elevator represents a dead end to the entire group.
Germans Love David Hasselhoff: This game sold much better in the States than it did in Japan. According to an interview about the sequel, Chunsoft analyzed that 70% of the viewers for the promotional video are English speakers. In fact, one of the reasons they greenlighted a sequel was because of the International fanbase. Germans love David Hasselhoff indeed!
Ho Yay: Some of Snake's dialogue suggests he's kinky and prefers men. Either that, or he's really good at trolling Junpei.
If Junpei enters Door 5, then examines the bed multiple times, Snake will comment on it.
Snake: Junpei, I cannot help but notice your interest in the bed. Perhaps you are hoping we will spend time on it, together...
Junpei: Gah! Y-You—! I— Don't say stuff like... damn! That's not a mental image I want!
In the Safe Ending, Snake's death is one of only two deaths in any of the bad endings that causes Junpei to completely flip his shit, to the point that he has to be physically restrained, then punched in the gut and carried out by Seven to keep him from running to Snake and locking himself in the incinerator. The only other character whose death has ever evoked that kind of extreme reaction is June, Junpei's childhood friend and love interest.
Iron Woobie: Snake... and possibly Akane, depending on your interpretation of her character.
June, a.k.a. Akane, who masterminds the entire plot and shows a considerable ruthless streak in disposing of enemies.
Junpei, usually classified as a Guile Hero, shows that he is capable of Magnificent Bastardry as well; he's just lacking enough opportunities to prove it. So go ahead, give the guy a chance. Insiston takingDoor #3.
The Funyarinpa.Explanation What? An explanation? You don't know about the Funyarinpa already? That's-that's practically blasphemous! Apologize to the Funyarinpa at once! ... A random word that Junpei comes up with on the spot. When the other characters don't know what he's talking about, he says more or less what you just read.
Upside-down sudoku.Explanation (spoilers) The final puzzle of the game is just a sudoku puzzle, but you have to flip your DS to see it upright due to the nature of the later twists.
Moe: Clover. When she hasn't gone crazy, that is. Or even then.
Junpei in the Safe ending, with his scream of "KAAAAAANNNNNNYYYYYYYYYY!" The pose doesn't help much, either.
The Ax ending is mostly rightly horrific save for the one shot of Junpei's face◊, which just looks unintentionally hilarious.
Seven, in the flashbacks of his rescue of the kids. His facial expressions while he's opening the grate are... amusing, to say the least, in sharp contrast with the situation.
The mostly excruciating Safe ending also provides one of the most inappropriate moments imaginable for a Metal Gear joke to make itself. I guess we can assume that "Snake! Snake! SNAAAAAKE!" would sound better if we could actually hear Junpei's voice. (And we can if playing the remake)
The localization is mostly excellent, but its extensive use of similes comes off as inappropriate during certain moments, such as Nijisaki / "Snake"'s death, which has his corpse compared to spaghetti and pizza dough.
Never Live It Down: Clover will always be remembered for completely breaking down and murdering everyone in the Ax Ending.
Snake's (fake) death, if you chose room 5. He is one of the most awesome characters in the game, and one of the most useful.
Snake's (real) death in the Safe ending. It's brutal, and the description (and accompanying sound effect) of Ace kicking Snake's face and upper body is cringe-worthy.
Santa taking June hostage may come as a bit of a shock, especially after he shares a bit of his past and the reason for his cynicism, and after he shows blatant (and apparently genuine) concern for June when she collapses. It's only later that it's revealed that his concern truly was genuine; taking her "hostage" was part of the plan, and his best chance at saving her.
Shipping: Akane and Junpei, obviously. There are some moments for Junpei and Clover, but not as much as with Akane. Also Lotus and Seven. The UST is so heavy you can feel it. Lotus/Seven has since been confirmed byWord of God. Also Santa and Clover – when he starts getting all excited about the stairs you're climbing and how they'd be perfect for looking up skirts, he immediately demands that you bring Clover over.
The Woobie: Everyone! Except for, you know, Ace and the rest of the Cradle Pharmaceutical guys. In particular, Clover, Snake, Santa and Akane.
Woobie, Destroyer of Worlds: Akane's own misery ended up turning her into a completely amoral mastermind willing to do anything for survival and revenge...and yet we can't hate her, after what she'd been through to begin with, and it was pretty much the only way she or anyone else could get out alive.