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  • Alternative Character Interpretation: The Shroobs. Are they really an Always Chaotic Evil race of Scary Dogmatic Aliens who exploited the toads for their own selfish gain as the game wants you to believe? Or are they actually a Destroyer of Worlds Woobie Species forced to obey Princess Shroob against their will and carry out her crimes against Toadkind out of fear of what she would do to them if they ever decide to form a La Résistance?
  • Anticlimax Boss: The Post-Final Boss against Shrowser is more of a fairly easy dodging minigame than an actual fight, a letdown in difficulty coming off the heels of two incredibly tough final bosses.
  • Awesome Music: See here.
  • Base-Breaking Character: Stuffwell. Some love him for his adorable design, funny dialogue, and for acting as the Bros.' suitcase. Others dislike his constant interjections into cutscenes and for being responsible for the massive number of tutorials in the first part of the game.
  • Breather Level: Coming between the battle against Petey Piranha and Toad Town Ruins is Thwomp Volcano/Caverns, which are fairly short, easy to navigate, and lack any particularly strong foes to battle on your way. The only semblance of challenge you might experience here is the battle against Bowser and his baby self, and even then, some Ice Flowers and Copy Flowers will take care of them eventually.
  • Complete Monster: The younger Princess Shroob is the acting ruler of the Shroobs, and debuts leading an invasion force to lay waste to the Mushroom Kingdom and depose Princess Peach. Under her heel, the Mushroom Kingdom is reduced to a charnel wasteland, while Toad towns and villages are depopulated so the Shroobs can suck out their life force to fuel their spacecraft, an agonizing and wasting process for the captured Toads. She also unleashes the Yoshi-eating Yoob on the Mushroom Kingdom, transforming whatever it eats into more Yoobs. Princess Shroob also makes a vile public spectacle of Princess Peach's attempted execution, trying to feed her to Petey Piranha in front of a bloodthirsty audience of thousands. Princess Shroob is the crowning example of cruelty even among her Always Chaotic Evil species, and is one of the most sadistic villains ever to appear in a Mario game.
  • Contested Sequel: While generally agreed to be a good game in its own right, many fans consider this game the weakest in the series after Mario & Luigi: Paper Jam, mostly because of its high linearity (which isn't helped by the lack of an interconnected overworld like the other games, instead having a Hub Level), often excessively long boss battles (though this was more serious in the American version, as the European and Japanese versions were released after and rebalanced the boss battles by reducing many bosses' HP), turning the Bros. Attacks into consumable Bros. Items and removing Bros. Points, that there's absolutely nothing to do after clearing the game, etc. However, many other fans say instead that it's the best of the series or one of the best, for its great core gameplay, its Darker and Edgier storyline, excellent and hilarious humor and characterization, like the bosses being long and hard, its relatively fast-paced nature compared to the other games, and don't mind its linearity. All of this said, the consensus seems to be that it's an okay game on its own, if not excellent.
  • Demonic Spiders:
    • Elite Boom Guys. They are very fast at the time of attacking, hit fairly hard, and can even fake-out so you jump at the wrong time, making their attack unavoidable.
    • Fly Guys. They carry bombs with a timer on them. When they attack, they fly to the top of the screen and drop the bomb on the Bros, which must be hammered back. The problem is, there's very little room for error, so if you fail, the bomb will hit you, either doing fairly large damage and possibly making you dizzy, or exploding and doing very large damage and almost ensuring you'll be confused, making you easy target for other enemies. At least their other attack is fairly easy to dodge.
    • Piranha Planets. Great amounts of HP, large attack stat and unpredictability (one attack is almost a carbon-copy of the Fly Guys mentioned above, while the other requires alternating button mashing) make them very hard enemies.
    • Shroob Rexes. These guys hit hard, and if you don't reduce their stature with jumping attacks in time, they'll have an unavoidable attack that will deplete a large chunk of your HP. They also appear along other Shroob Rexes and Yellow Bubbles (see Goddamned Bats below for more information).
  • Ending Fatigue: No fewer than three final bosses, and two of them have too many hit points. And there's still a Post-Final Boss after this.
  • Game-Breaker:
    • The Ulti-Free Badge, available at Fawful's Bean 'n' Badge for 90 Beans, gives you unlimited Bros. Items on whoever's wearing it with no restrictions whatsoever, allowing the player to never have to use normal attacks again.
    • Copy Flowers and Trampolines. The general idea of both is the same: with proper action command timing, you can keep going indefinitely, making it possible to deal stupidly large amounts of damage to enemies with one use.
    • Mix Flowers. One of the final Bros. Items obtainable in the game (can be bought in shops once the player reaches Toad Town, and can be found in item blocks throughout Toad Town, Star Hill/Shrine, and Shroob Castle), it has the four bros tossing fireballs in the air to create a giant fireball, which, when it gets too low and the attack ends, explodes on the group of enemies and heavily damages them all. It's capable of decimating entire groups of enemies in one hit, and is easier to execute than Copy Flowers and Trampolines. The only reason why it's weaker than Copy Flowers and Trampolines against bosses is because it caps at 999 damage, whereas they don't have a damage cap, meaning a skilled player can deal thousands of damage to a boss with them.
    • EXP Badge A, available at Fawful's Bean 'N' Badge for 70 beans. The bro that it's equipped to gains 40% more EXP from enemies killed by Bros. Items. Farming beans in Thwomp Caverns to obtain 280 beans and buying 4 of these to equip to all 4 bros means the entire party will receive the 40% EXP boost from enemies killed by Bros. Items. If you stock up on beans in Thwomp Caverns before completing the level, go back to Fawful's Bean 'N' Badge and purchase 4 of these, then proceed to Toad Town and stock up on loads of Mix Flowers, every battle becomes an extremely easy EXP grind that will make all the bros overleveled for the remaining boss fights.
    • Drain Badges, which heal you for a small amount every time you score a hit. For regular attacks, this is pretty insignificant... but they also count for every hit of a bros. item attack, including the ones that can go indefinitely. Even an average player can easily heal for half the user's HP or more, making you virtually unkillable if you use bros. items continuously.
  • Goddamned Bats:
    • Shroids. They have one attack that is very annoying. It takes two flags, and the bros must jump/do nothing depending on color raised, performs this multiple times (up to six), and one failure results in an unavoidable attack. Also, it may summon a UFO that drops a spikeball, countering this causes the Shroid to malfunction. This means the "flag" attack from earlier is reversed- the other brother needs to jump for each flag raise.
    • Ghoul Guys. Not very hard to kill, but they can sacrifice themselves to make a Fusion Dance with another enemy in the field, making it much more stronger, faster and resistant.
    • The Skellokeys are just like normal Pokeys... except they are spiny enemies, meaning you must destroy their lower sections first, one by one, unless you don't wanna waste one of your Bros. Items. Their attacks are also very unpredictable and generally appear only for the babies, which aren't the best fighters in solo mode.
    • Thwacks and Wonder Thwacks. They appear in fairly large groups (up to eight) and can call even more of them, making them fairly large annoyances.
    • Love Bubbles and their upgraded versions, Soul Bubbles. Very unpredictable attack patterns and the ability to heal other enemies make fighting against them a tough task.
  • Good Bad Bugs: In the underground area under Gritzy Desert, there's a floating platform in one room. If you have just Luigi jump onto it, and then stop moving, the bros begin spazzing out and teleporting around, potentially ending up in a hill and getting stuck or separating the bros across the room. If you do get stuck, there was a Save Block in the last room, so there shouldn't be too much progress lost.
  • Hilarious in Hindsight:
    • The entire plot of this game centers around the Marios and Bowser fighting off aliens. Fifteen years prior, an episode of The Adventures of Super Mario Bros. 3 had the entire Mushroom Kingdom, including the Koopas, panicked about an alien invasion. Turns out those "aliens" were just a human family from the real world.
    • The Super Mario Bros. Super Show! episode "Two Plumbers and a Baby" involves Peach getting transformed into a baby after falling in the Fountain of Youth. Sixteen years later, Baby Peach makes her first canon appearance in this game; coincidentally, Toadsworth at one point even believes his past self has transformed Peach into a baby to kidnap her.
  • It's the Same, Now It Sucks!: Some critics felt the gameplay didn't innovate enough, being essentially Superstar Saga with a more linear overworld and babies tagging along. Adding fuel to the fire was the fact that there was only one segment that utilized the DS's touch screen, which felt tacked on.
  • Memetic Mutation: After the release of Splatoon (and especially after this game's Virtual Console release), many people joked on Miiverse that Nintendo had been planning about making Splatoon for over ten years through Young E. Gadd's comment:
    Young E. Gadd: I have an inkling I'll be seeing you again soon... Bye!
  • Narm: The destruction of Hollijolli Village can come across this. Evidently, the developers decided that the Shroobs should literally destroy Christmas to convince us they're evil.
  • Narm Charm: The atmosphere of the desolate, ruined Hollijolli Village is a perfect introduction to just how brutal the Shroobs are, and more than makes up for how on the nose it is.
  • Nightmare Fuel: Enough for its own page.
  • One-Scene Wonder: The sequence with the mind-controlled Hammer Bros. who speak exclusively in 1337 is easily one of the most memorable moments in the English script.
  • Padding: Bosses having far too much HP. This was notably only done in the American version, with the European and Japanese versions (which actually came out after the American version) being more reasonable. For example, Princess Shroob has 1700 HP in the Japanese version, because they knew a boss constantly protecting herself with a barrier didn't need 3000 HP.
  • Porting Disaster: The Wii U Virtual Console release. Like all DS games on the Wii U Virtual Console, the default screen setting is an incredibly tiny virtual representation of a DS that you can barely see unless you're staring at the GamePad, and even then you can barely see it. And the only ways to increase the screen sizes involve separating the screens in some way, either by enlarging one screen and putting the other screen next to it on the side, or by having the top screen of the DS on the TV screen and the bottom screen on the Gamepad. On most DS releases on the Wii U Virtual Console, this isn't really a problem, but in this game, 80% of battles have attacks that go across both screens (from both the Bros. and the enemies and bosses), so if you set it up any other way than the default it becomes harder to counter or use attacks properly, and if you use the default settings you can barely see any of it anyway. This makes the game needlessly difficult on the Wii U Virtual Console release. This can be mitigated by zooming in on the TV screen with the default Virtual Console settings however.
  • The Scrappy: The Star Gate gets a lot of hate for being an unreasonable jerkass to Luigi. Even though he later admits that he was only doing it to see if Mario would defend him, his cruelty to Luigi only (i.e. honest-to-goodness gaslighting the poor guy by giving him three options to answer a question, calling them all wrong, declaring the answer an unavailable fourth option, and accusing Luigi of lying when he points out that said fourth option did not exist for him to pick) rubbed fans the wrong way. It doesn't help that Luigi's treatment during the game before this point already comes across as mean-spirited.
  • So Okay, It's Average: The game is generally thought of as "good", not too good but not at all bad either. While having excellent writing and characterization, an interesting Darker and Edgier spin on the formula, as well as its great core gameplay and its relatively fast-paced nature compared to the other games, the game is let down by extremely linear progression and area design as well as overly long boss battles, along with the Bros. Attacks becoming one-use items and nothing to do after the game's completion; which some fans mind while others do not. However, most fans feel that the game isn't bad by any means, and can be enjoyable at least for a single playthrough.
  • Sophomore Slump: While still thought of as a good game, many fans consider this one weaker than Superstar Saga, due to the fully explorable world being replaced with a more linear set-up and due to the controls getting a little convoluted what with all the switching back and forth between A/B and X/Y. Probably the reason Bowser's Inside Story returned to the explorable world and kept the A/B and X/Y portions completely separate.
  • Squick:
    • There's an organic structure leaking water like a fountain inside Yoob's lower gastrointestinal system that you need to make Baby Mario drink from. This doesn't go unnoticed in the official strategy guide, which refers to it as "delicious Yoob water".
    • Again regarding Yoob, you are able to have the baby Bros. drill into his flesh while inside of him. To make this even more gross, Yoob winces in pain on the map screen every time you do this. Because there are a lot of Beans inside of Yoob, you'll be doing this a lot.
  • That One Boss:
    • The battle against Bowser and his younger self is surprisingly difficult compared to the previous bosses, since their attacks are somewhat difficult to dodge, they utilize combination attacks with several fake outs, and they hit hard. Add the fact that they heal each other almost every time, and you have a true climatic boss of a volcano.
    • Also, Petey Piranha, while not as hard as the battle in Thwomp Volcano, switches between being flying and spiked and takes some time to learn the tell for his flying attacks. Also, he's one of only three bosses in the game who is only one target to attack multiple times a turn. It should be noted that the Bowsers and Petey are the two Climax Bosses.
    • Transformed Elder Princess Shroob has extremely high HP, an extremely high rate of attack with attacks that are difficult to dodge, and requires several other points of her body to be attacked before you can even target her actual source of HP. You also don't get the mercy of Peach occasionally healing you like in the first phase, as she's knocked out before the second phase starts. Even for the standards of a Final Boss, she is practically unstoppable if you aren’t high-leveled enough, and has without doubt caused many a player to Rage Quit the game entirely if they aren’t leveled up to a point that she is remotely possible to beat. This make sense in-universe as fighting to avenge both her sister as well to save her species from extinction would undoubtly make her Defiant to the End.
  • That One Level:
    • Toad Town Ruins. Remember Joke's End sequences from the previous entry where the Bros had to explore alone for a good chunk of the dungeon? Well, Toad Town Ruins might be arguably worse, since almost the entire level involves the Bros and their younger selves being separated the whole time, with special mention going to the Babies' parts, as they are considerably weaker than the adults which makes battles longer and tougher. With their lack of strength and defense and low HP, they can easily be killed, especially Baby Mario. And for extra fun? Every enemy here enters the Goddamned Bats category (see above), featuring Shroids, Skellokeys and Love Bubbles. Shroids have annoying attack patterns, Skellokeys can't be jumped on and, are unpredictible, you have to destroy their segments first and are among the few enemies that onnly the babies can fight, and Love Bubbles have umpredictable attack patterns and heal other enemies. Prepare for a lot of pain when crossing this place. At least there isn't a Boss Battle to worry about though.
  • Underused Game Mechanic: Though it is a DS game in a series known for using each console's unique capabilities in one way or another, as it was released just a year after the console launched, the touch screen isn't used at all for about 99% of the game. The only time you use the stylus is when you remove dirt from a drawing to reveal two Princess Shroobs. Tellingly, Bowser's Inside Story and Dream Team use the touch screen to a far greater extent.
  • Unintentional Period Piece: The Leet Lingo used by the Hammer Bros. firmly dates the game to the early/mid-2000s, as 4chan-based jargon started taking its place around 2007 and had completely displaced leetspeak in the cultural consciousness by 2008.
  • Unintentionally Sympathetic: The Shroobs (barring the younger Princess Shroob) have garnered sympathy from the fanbase in recent years, sometimes to the point where a few fans outright reject the ending for killing off the species with the exception of a few surviving remnants in Bowser's Inside Story. See The Woobie below.
  • Unintentionally Unsympathetic: The Star Gate. Apparently, his poor treatment of Luigi was just a Secret Test of Character on Mario to see how he'd defend his brother. However, this reveal can make The Star Gate come off as even less likable, as his bullying towards Luigi comes off as completely unnecessary and too harsh. Luigi had already been abused throught the game which The Star Gate should know since he was looking into his soul, but goes on to "test" him anyway.
  • The Woobie:
    • Peach. It's one thing to have Bowser kidnap her knowing Mario will routinely rescue her, but here a hostile alien race doesn't have the same concern for her as Bowser to keep her unharmed, at one point feeding her to Petey Piranha for a quick laugh. Also, while Bowser would only storm into her castle and kidnap her, the Shroobs are the first antagonists to attack her entire kingdom, and she's powerless to stop them.
    • Luigi spends the entire game accumulating physical and emotional abuse from the enemies, the characters, the setting, his main allies, and especially the Star Gate.
  • Woobie Species:
  • Woolseyism: Let's face it, would this game really have the Hammer Bros. talking in 1337 in the Japanese version, saying things like "ROFL" or "PWN"? note 

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