The episode marks a base under contruction from Star Fox: Assault in Sector Z instead of the ambush of Great Fox in Star Fox 64.
The Blue Typhoon and the Great Fox heading through Sector Z. Sonic says that the Star Fox Team always remember during the first Lylat Wars. Chris states that the Venomian army are building a space base in this sector. The Star Fox Team take off to infiltrate Sector Z, the remains of Sauria that Cornerians removed from Dinosaur Planet into Sector Z. In the Crimson Egg, Doctor Eggman remembers during the First Lylat Wars when Copperhead missiles target Great Fox. The Blue Typhoon detects the Chaos Emerald inside the base. The Star Fox Team through a graveyard of wrecked warships and enter a base under construction. When they find the White Chaos Emerald, they confronted by Andross' bioweapon, the Biobrain. It is the 1st form of the cores found in Sector Z which shut down enemies according to R.O.B. 64. In order to defeat the Biobrain, Fox must destroy the 5 triangles around it, then attack the Biobrain itself. As Fox attacks the Biobrain it divides like a cell. Doing a Barrel Roll stops the Mini-Biobrains from hurting the Arwing II. The Star Fox leader also gains boost gauge by doing this. After defeating it, the Biobrain assimilates and becomes fused with a large spacecraft, using its large grabbing arms to hurl meteoroids at them. Fox fights and destroys the Biobrain, and retrieves the White Chaos Emerald. Just before the team departs to Venom, Krystal receives a sudden distress call from Sauria, the Dinosaur Planet, which is under attack by the Venomian army.
- Sector Z has a more dark purple shade compared to Star Fox 64's orange.
- "Fichina & Sector Z" theme is replaced by "Sector X" theme.
- Defending Great Fox from missiles is replaced by invading the base before it could be completed.
- The boss of Sector Z is the Biobrain from Star Fox Command.
- When the Biobrain fused with machinery, it strongly resembles Gorgon and an Aparoid-infected Pigma, having similar attacks and defenses. Also, its core resembles the center of the Aparoid Generator.
- "Briefing 2" - Star Fox: Assault
- "Sector X & Sector Z" - Star Fox 64 3D
- "Boss Battle 2" - Star Fox 64 3D
- "Mission Complete" - Star Fox 64 3D