Unmarked spoilers below!
Bowser and the Koopas' Staff
- Mario and his friends holding a funeral for Luigi when the hand wand made him disappear to the Underwhere.
- Koopa dejectedly remembering all the good times he had with Bowser after he was selfishly tossed aside.
- Goomzilla has confirmed that Crazy Hand succeeded in eating the Goomba that helped Koopa get back home.
- Bowser's willingness to have Goomfrey beat Peach with a baseball bat in Part 2, just for looking at his diary. And since he loves her, this is straight-up Domestic Abuse. Goomfrey, however, couldn't bring himself to do it, and cries uncontrollably instead, as pictured on the right.
- Yoshi getting crushed by a pyramid while trying to protect one of the stars in Part 3. Thankfully, said star was keeping him alive long enough for him to stop Bowser.
- Toad losing his train in Part 4, but as he puts it, "at least we didn't lose our lives as well."
- All of Whacka's scenes had characters hitting him at no provocation. Except Peach and Goomfrey, and in return, Whacka protects them from a Boomerang Bro, costing him his life in the process. Once all of the heroes return home, they hold a funeral for Whacka. Unlike Luigi's funeral from earlier, this is dead straight, with no revival in sight.
- Goomfrey leaving Peach because "humans and Goombas should not mix". He says he's grateful for everything, but Peach was clearly depressed by his leaving.
- Francis crying when Luigi accidentally breaks his limited-edition Lady Bow poster. Even he and Captain Toad realize that they went too far.
- Solus' backstory. Once Bowser's closest minion and a fully-fleshed Koopa Troopa, Solus had a terrible accident and fell into the lava, burning off his flesh and turning him into a Dry Bones. Matters were worse when Bowser doesn't recognize him, and later throws him out of his castle. This made Solus so furious he sees the entire world as selfish. His evil actions are still inexcusable, but how would you feel if you were burned alive and unrecognized?
- By the end, we learn that Solus calling him selfish has hit Luigi particularly hard. Thankfully, the guardians of the Energy Cells assure him that that's not the case when they send their regards to him.
Yoshi and the Lost Egg
- No Gamebook story would be complete without a Downer Ending or two, and some of these endings can be pretty darned depressing. How bad can they be? Well, let's discuss them.
- The Bowser Ending isn't the worst ending, but it's still pretty bad. In a cute Call-Back to Paper Mario, Kamek asks you to truthfully answer which of the three things Yoshi hates the most. Picking Bowser over the Super Mushroom and Francis was obviously the most truthful answer, as Yoshi shivers in fear before he enters the door, as opposed to entering with more confidence after picking the other two choices. The more Genre Savvy audience should probably know that answering truthfully in this type of situation is a mistake. And it shows, as Bowser orders Yoshi to be locked up in a cage, while two Goombas mercilessly taunt him. Oh, and the Blue Yoshi is also forced to sell her nest for rent. Only one Yoshi Cookie is rewarded here.
- The Anarchist's Ending is undoubtedly the worst ending of them all, with Yoshi bowing before Wario and Waluigi to swear allegiance to them. He proves his loyalty to them by tricking the Mario Bros. into enslavement by the two creeps, in the process forgetting that he had a stolen egg to recover. This wouldn't be so bad if it weren't for the cheery voice clips Goomzilla played for Yoshi while this was going on, indicating that he was happy to do all these horrible things. This is all wrapped up with the Blue Yoshi getting a hefty scolding from the Village Leader for not watching that egg. No Yoshi Cookies to be found here.
Mario's Unexpected Transformation
- Mario's Imagine Spot which shows Peach outright rejecting Mario, now that he's a Goomba.
- However you feel about Bowser, he has it pretty rough in this movie. His strength was taken from him by a mysterious new villain, his minions don't recognize him and attack him, and he loses control of both his castle and his minions to the Duplighots. Even Peach can't help but feel bad for Bowser here.
- Koopa, believing Bowser to be dead, lays a bouquet of flowers for him in his planning chamber.
- The captain of the Great Glory in general. His parents fought in a war, and he was raised by a Duplighost who adopted him. The Duplighost gave him a book to remember him by, and he swore to protect it the way he was protected. Now that Peach and Bowser want it to defeat the Duplighosts, the captain won't give it up without a fight. But despite everything, he lost in the end, and is so broken that he doesn't even have the heart to escape the sinking ship—which was also partially his fault, as he let it happen. After a forgiving Peach saves him, he chooses his family life over the sea.