One of Star Fox Adventures' most infamous scenes comes during the final Krazoa Shrine at Krazoa Palace; just as Fox is about to engage in combat with General Scales (seemingly the game's main antagonist and final boss) the encounter is abruptly cut short. The spirit of Andross suddenly appears, interrupting the fight and forcing Scales to hand over the last Krazoa Spirit to Fox as Scales falls to the ground defeated and seemingly dead, effectively ending the confrontation before it even begins. According to a February 2008 edition of Rare’s Scribes, a proper boss battle against General Scales had originally been planned, but due to the impending Microsoft buyout, which was officially announced in September 2002, the team was forced to scrap it and focus exclusively on the final battle with Andross.

However, looking deeper into the development history of Dinosaur Planet and Star Fox Adventures, reveals a more complex picture regarding Scales' intended boss fight. The Dinosaur Planet condensed story promises a true final confrontation between Krystal and General Scales within the Desert Force Point Temple, as she places her final SpellStone. After Scales' defeat, the King EarthWalker would barge in and tell Krystal to take his belt (that was provided by Drakor), but then it would turn into stone, resulting in the player into having to swap over to Sabre's story, who takes it to the mutant Shabunga in Willow Grove to help reactivate it, which allows him to enter Dragon Rock unharmed.

Yet, in the leaked December 2000 build of Dinosaur Planet, this boss fight doesn’t exist. Instead, after Krystal places the final SpellStone, a cutscene plays where she, Scales, and Kyte are teleported outside the temple. Krystal lands safely in a pond, while Scales crashes onto a rock and injures his back, leaving him incapacitated. Instead of the King EarthWalker, it's the BoneHead SpellStone guardian who first appeared in CloudRunner Fortress that instructs Krystal to take the Kamerian belt to Sabre so he can have Shabunga revitalize it, as Scales whispers that he'll have his revenge as he passes out.

When the game transitioned to Star Fox Adventures on the GameCube, there were still signs that Rare hadn’t completely abandoned the idea of a Scales boss fight. Unused voice clips and data found in the 2002 E3 kiosk build suggest plans for a rematch with Scales aboard his flying galleon, similar to the prologue battle. However, this time, Fox would pilot the Arwing instead of Krystal riding the CloudRunner. Notably, Falco was set to appear much earlier in the story to assist Fox during this aerial battle. After defeating Scales, Fox would land at Krazoa Palace and partake in the Test of Sacrifice, the true final Krazoa test.

By the time of the 2002 E3 kiosk build, it seems Rare had already abandoned both the planned galleon battle and the Test of Sacrifice. Instead, they were experimenting with a one-on-one, on-foot boss fight against General Scales, taking place in the last Krazoa Shrine where the Test of Sacrifice was planned. While the encounter is clearly incomplete, it offers a glimpse of what could have been. In this version, Scales actively engages the player—unlike in the final game where he simply approaches Fox and assumes a fighting stance. He showcases several unique animations not seen in the finished release, including blocking, flinching from attacks, and even a brief defeat animation. Interestingly, the arena is populated with SharpClaw soldiers, suggesting that the fight may have originally been designed as a multi-phase battle, where players would fend off waves of enemies alongside the duel with Scales.