Just as Lilac (or Carol) is about to remove the Kingdom Stone from the Dreadnought's power core, Lord Brevon appears with Milla in his grasp and holding a knife to her throat, forcing her to remove Torque's hacking device from the core for the sake of her friend's life. With the ship's power restored and the Kingdom Stone relocated, Brevon destroys the device, drops Milla and leaves the room. Lilac (or Carol) tries to comfort the frightened Milla, whose eyes start to glow blood red, much to Lilac's (or Carol's) shock. She then transforms into a Mutant Monster, beginning the Boss fight where Lilac (or Carol) is forced to fight her mutated friend.
Mutant Milla is a larger, mutated version of Milla herself: being a quadrupedal mutant canine with a color scheme of ivory-white, orange and bright green. She has 2 large spikes on her back, a pair of snake-like fangs and her eyes are repositioned vertically with no mouth or nose on her face. Mutant Milla's tail has scorpion-like traits, as it curves upwards and has 8 claw-like appendages which she uses to fire her Shield Bursts & Phantom Cubes.
Mutant Milla will simply walk from one side of the room to the other, switching between attacks as she does. Whenever she takes damage, she will drop a Health Petal, and will start Puppy Floating afterwards. When close to being defeated, one of Milla's eyes will break, just like in the Boss Fight with Mutant Serpentine.
- Shield Burst: Mutant Milla will fire a burst of shields from her tail, widening in and out as they move across the room.
- Phantom Cubes: Mutant Milla will fire 3 Phantom Cubes from her tail at random angle; bursting upon hitting the ground.
- Super Shield Burst: Mutant Milla will run around the middle of the room, firing Super Shield Bursts from her tail and dealing damage under and above the Player.
- Puppy Float: After taking quarter damage, Mutant Milla will Puppy float in the air and fire 3 spread shots of 4 Phantom Cubes from her tail.
Once she's defeated, Milla will turn back to normal, but falls into a death-like coma. As a result, Lilac (or Carol) becomes enraged and she goes after Brevon, eventually defeating him. After the Final Battle, Milla is taken to the Snowfields, where her injuries are treated by Neera Li. She wakes up from her coma, apologizes to her friends and starts crying out of guilt for attacking them. Lilac tries to comfort her and ease her guilt, while Carol also starts to break down in tears.
In Milla's Story, this Boss Fight doesn't happen, since she's playable in this Round and the next. Instead, she enters the Dreadnought's power core and is shocked to find Torque with an unconscious Carol. He explain to her that Brevon had ambushed them and Lilac went after him alone. Learning of this, Milla resolves to help Lilac and goes after her, promising Torque to keep an eye on her while he takes care of Carol.