Even for a comedy cross over game with Mario and the Rabbids coming together, that is not to say that it is completely devoid of scary moments, because both series have a history of having their fair share of creepiness to some degree.
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- During the ceremony where Mario and his friends were unveiling a statue of Princess Peach, it quickly goes awry when Mario sees a vortex forming in the sky at the same time the Rabbids from another universe arrive. You can see the Toads screaming as they are pulled skyward into this vortex and the ground below Mario cracks as his friends and even his own brother ends up being caught by its gravitational pull. You can see just how desperately the Mario Bros. reach out to stay together, which fails.
- After Spawny managed to merge several Rabbids with various objects, he gets the full brunt of the Supa Merge's power and ends up fusing with the device itself. He noticed this and tried to take it off once he realizes its dangers, but it ends up being permanently stuck to his face. Even worse, is that whenever he is stressed out, he will lose control over those powers and end up merging a Rabbid with other objects.
- It gets even worse is that Bowser Jr. noticed that Spawny had this power, he takes him along and forces him to use his power to create an army of Supa Merged Rabbids that he can use to take over the kingdom. The icing on top? The vortex is actually taking on the form of an entity that is the Megabug and it steadily forms when energy is suffused into all of the corrupted Rabbids wreaking havoc on the Mushroom Kingdom; and when that Rabbid is defeated, it splits into its components before sending the residual energy to the Megabug, essentially granting it more power that would end up causing mass destruction. And the heroes were forced to defeat them since their presence is a serious threat, and as they are neutralizing them, it also ends up helping the Megabug take on a new form. Beep-0 even stressed the importance on saving Spawny before his power ends up causing mayhem.
- With the exceptions of Rabbid Mario, Rabbid Luigi, Rabbid Peach, and Rabbid Yoshi, the rest of the Rabbids that were merged after arriving at the Mushroom Kingdom have all become corrupted by the Supa Merge's power and they end up behaving much more maliciously than they were ever before.
- The second act of the final level, that is the Lava Pit, is much darker toned than any of the previous levels, especially after Bowser Jr.'s defeat, which results in Spawny falling towards the abyss, much to Jr.'s dismay as he leaves. Had Yoshi not caught him in the nick of time, Spawny would have faced a horrible death.
- After Spawny spends a good amount of time with the group after befriending them, he is hypnotized by the strange energy emitted by the Megabug, who then absorbs him and flies away to Bowser's Castle. As a result, it grew strong enough to create several high-ranking minions, Bwario, Bwaluigi, and the Lava Queen, to hold them off while it was gaining power that would result in the world being destroyed.
- Mega Dragon Bowser is absolutely horrifying; due to his son's part in making Spawny create an army, it resulted in the Megabug taking on a draconic form and takes full control of Bowser, who sprouts wings and has glowing yellow-colored eyes that look totally MENACING! It doesn't help that his typical roars end up sounding much more demonic than it normally is and it is just creepy.
