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- Anticlimax Boss: Certain mice are easy to catch and yield enormous rewards of points and gold, but getting into position to catch them is very difficult and requires a lot of time and expensive cheese.
- The Eclipse Mouse, if you have the right weapon. With a description stating that it is darkness and fear itself, it sure doesn't put up much of a fight if you wield the Ancient Box Trap. In fact, his difficulty rating is "Effortless" is you do so — the lowest possible.
- The Mystic King, Technic King, and Chessmaster mice are much easier to capture than the respective Mystic/Technic Rooks or Queens, just like a real chess game.
- Archive Panic: There are over three hundred different mice to catch, not counting limited edition or Special Event mice. Happy hunting!
- Demonic Spiders:
"Hunter's lore describes these mice as a curse, bringing bad luck and fruitless hunts. Hunters lament at the eerie caw of a Harpy mouse descending from the clouds, knowing that escape is impossible. Harpy mice exist to torture Mouse Hunters by constantly stealing their cheese and raiding their supplies. Their swift wings bring a dark plague of frustration to any hunter unfortunate enough to encounter them"
- Harpy Mice in the Lagoon. Players would've most likely brought either a Physical, Tactical or Hydro trap, while their main weakness is Shadow, and their mouse power is very high. The Harpy's description even Lampshades this:
- Vampire mice in the Mousoleum and the Catacombs. They give you very little gold and points compared to the other mice there. If they happen to steal your gold, they steal a lot more than the other mice.
- Fridge Horror: The Warmonger mouse sends in the new recruits on the first wave before sending in the more experienced soldiers on the next two. In short, the inexperienced mice who wanted to join (or were forced to join) his army are literally being sent to an early death!
- Justified for the new scouts, as they are "trained" by being thrown directly into the first wave of the battle instead of spending months on the training grounds.
- The whole concept of catching and killing thousands of sentient living beings. Some of those traps are horrifyingly cruel.
- Game Breaker:
- Many Limited Edition traps have respectable Power and stupidly high Luck. Luck also determines whether or not you succeed in catching a mouse, and the effectiveness of luck rises exponentially. Of note are the Partybot (Physical), Chrome Deathbot/Drillbot (Physical), Giant Speaker/2010 Blastoff/Rewer's Riposte (Tactical), and Kraken Chaos/Double Diamond Adventure (Hydro)
- The Oasis Water Node trap, the Sphynx Wrath and especially the Sandstorm Monstrobot trump all of these. However, if you want those three traps, you will have to Earn Your Fun.
- The Phantasmic Oasis trap, Grand Arcanum trap and the Clockwork Portal trap also count.
- Internet Backdraft: In the past, when the name Ronza was mentioned, the forums would go crazy. Nowadays, there's no such insanity, but it continues to be parodied.
- Scrappy Mechanic: Cursed City Minigame. It requires the player to actively switch between 3 charms after each successful catch to dispel 3 curses to allow another mouse with better loot to be attracted, but Corrupt mice can waltz in at anytime and reset all the curses, even if he's caught. After successfully dispelling all 3 curses, yo uare given a grace period of 3 hunts where Corrupt can not be attracted, but after that, Corrupt will reset all your work when attracted. Some take days to even manage dispelling all 3 curses.
- Made worse when you're hunting for the Dark Magi boss. He can only be attracted after dispelling all 3 curses and equipping a charm, and that charm will also cause only one other mouse to be attracted: The Corrupt.
- Tear Jerker: Greedy Al is an embittered Jerkass by the time you confront him during the Great Winter Hunt, but the letters to Santa he wrote when he was young and disappointed by empty stockings are heartbreaking.
- That One Boss:
- The Acolyte mouse. The Dragon, Big Bad Burroughs, and Silth are starting to give it competition, though.
- The BBB is not so bad. At least the mice in the area where its found in cannot steal anything from you. The others...
- That One Level:
- Depending on whether the "Devs Hate U", each run in the Zugzwang's Tower can be a big failure, or success, or anywhere in between.
- The Dreaded Horde in the Jungle of Dread are made to be especially hard. Even with the best traps for that location (such as the Cackle Lantern and the Clockapult of Time), you will fail to catch them over half the time.
- Ugly Cute: The Itty-Bitty Burroughs mouse.
- "Funny Aneurysm" Moment: William Hickey, who plays Posthumous Character Mr. Smuntz, died before the film's release.
- Nightmare Fuel: The painting of their father is moody throughout the film, but then magically changes to a grin, when the sons finally work together for real. In intention, a beautiful event to show the father being proud of his sons even after death, but the goddamn painting changes through supernatural forces. Not intentionally scary, but if you think about it, it's chilling.
- And as proof of YMMV, this same moment can also come across as intended, as a wonderful Crowning Moment of Heartwarming. Particularly when paired with the recurring theme of "teamwork and sharing are good things", Ernie finally earning his father's pride, and the Arc Words "A world without string is chaos."
- A more chilling example is when the brothers enter the city pound to find a cat, and there's a little girl being dragged out by her mother screaming about her kitty being left behind...the kitten is taken inside, and the room fills with smoke hopefully for decontamination... It doesn't help that a great deal of the imagery, music, and visual cues are reminiscent of the Nazi death camps, surely intentionally so.
- One-Scene Wonder: Christopher Walken has an extended cameo as an expert exterminator, who, of course, fails to take down the mouse. This being Walken, it goes without saying that the character is an eccentric Large Ham who takes to pest control like a member of a SWAT team.
- Squick: Eating the cockroach.
Lady: The raisins are a nice touch.Ernie: (Smiling) They're good, aren't they? (Takes two steps, and stops.) Raisins?
- Right before the big finale...
- For those who don't get it, the "raisins" were the mouse's droppings.
- Caesar voluntarily EATS one of the mouse's feces!
Caesar: Slight potassium deficiency.
- Spiritual Licensee: Could be considered a better Tom and Jerry movie than the Tom and Jerry movie.
- The Woobie: The brothers, considering everything the mouse puts them through.