After defeating the 12 rare Zodiac Monsters (the most difficult and time consuming task to do) that appear after beating the game, a special alternate ending to the game will play where six female characters (Holly, Colt, Viola, Minta, Crysta, and Miss Sapphire) confront the player, Errick and Cleo, with Holly and Colt stating they rounded "everyone" up to celebrate the defeat of the Zodiac Monsters. Their extremely suggestive praises of the player and anticipations of celebrating "tonight" (with Viola commenting she wants to see what makes him "tick") anger Cleo who feels that she is not being given proper credit for her work, suspects something is up, and tries to save him from the encounter, but she is attacked by Viola and appears to fall unconscious before he is "captured" and taken away by the six women. What then occurs is a fade-to-black followed by the "rest" theme that plays when you let a monster rest for the week, and the sound of two owl hoots. The scene then cuts to the following morning, where Errick remarks that he is jealous of the player and Cleo returns demanding to know what the player did the prior night as Holly and Colt giggle. She angrily denies him supper for a month, with Holly commenting she will give him some of hers behind Cleo's back.

This cutscene explicitly implies that the player partook in a harem orgy, with Colt in particular implying that the player took her virginity. Monster Rancher DS was rated E for Everyone by the Entertainment Software Ratings Board (ESRB), but their rating still points out the game features "Mild Suggestive Themes". It's unknown if this warning was added to refer to this scene or if the game's publisher intentionally left out this scene when submitting content to the ESRB for review.