Yakuza engages Samus as she attempts to reactivate the station's reactor. Samus ventures into a large, empty silo, and falls to the bottom. An explosion comes from above, and Yakuza fires upon Samus. It then begins crawling around the silo, trying to grab her; if Yakuza manages to grab Samus, it will carry her upwards while injuring her with its front legs, and she must struggle wildly to free herself before Yakuza can drop to the ground and crush her, causing heavy damage. If Samus were to switch to her Morph Ball form and stay in the lower left of the battle area, the Yakuza would be unable to pick her up, therefore saving energy for the second phase. Samus must fire Missiles or charged shots into its periodically open mouth to damage it, then dodge the fireballs that come out. Once Yakuza has taken enough damage, its legs will fall off and its head will begin using an ability identical to the Space Jump to fly around the room by spinning. It pauses quite often to spit out worm-like projectiles. Yakuza's open mouth is vulnerable to attack at the height of its jumps, but is not exposed while it is spinning. Eventually, Samus destroys Yakuza, and eliminates the shell of its Core-X.
By absorbing the Yakuza's Core-X, Samus regains the Space Jump ability. She jumps up into the shaft that Yakuza revealed, and restores the auxiliary power to the station.
- It is unknown whether the boss was literally using the Space Jump item or if it was using a natural ability found within its species that allow it to fly similarly to said Chozo item, but it is also possible it is using the wall seen in the background to move about as its legs are constantly moving.
- Yakuza is not an actual spider. Yakuza has three pairs of legs and an odd number of eyes, along with a non-segmented body. A true spider would have four pairs of legs, an even number of eyes, and a body with two body segments.
- Yakuza is a generic term for organized crime syndicates in Japan, much like the term mafia elsewhere.
- It appears that Yakuza has a damaged left eye, or that its eyes grow asymmetrically. It shares this trait with the Gullugg.
- In the beginning of the battle, once Yakuza fires the first volley of fireballs before it climbs down, it is vulnerable to attack. Yakuza is actually directly above the viewable screen of the battle chamber when the battle begins, and its opened mouth is highly vulnerable to attack. Jumping up from between two of the now-landed fireballs will give Samus a good position to fire Missiles diagonally into its mouth. Exploiting this secret well can cause Samus to bypass nearly half of the first phase of the battle, causing Yakuza's color scheme to transition directly to purple from the start.
- This battle is the only time Samus sees a golden Core-X.
- On Easy Mode (in the Japanese version only), Yakuza will not fire projectiles during its second phase.
- It shares the same boss theme as Serris.
- It is possible that Yakuza fed on electricity. This would explain it emerging from the corridor leading to the Auxillary Power Room.
- During both phases, it is possible to hit Yakuza's mouth from the side instead of diagonally or from below.