Sanctuary Fortress is comprised of two levels, connected by several elevators. The area's puzzles and enemies make heavy use of the spider ball, seeker missiles, and the boost ball. Samus finds the spider ball, echo visor, screw attack, and (in the dark world) the annihilator beam in the Fortress.
Four-legged sentry units with separate head (CM) and body (MB) modules. Each piece can be destroyed independently of the other. Quads possess sweeping laser beams and can perform a spin attack which can be halted by boosting into the spinning mech. After being hit with the boost ball, a red light extends beneath the Quad. Boosting through this node will destroy the Quad's body and cause the head module to detach. When floating on its own, the CM will shield itself with either a white or a purple shield, which can be disrupted with the opposite color beam. Once the shield is down, a single super missile will destroy the head. The CM can launch energy bursts and even attach to nearby dormant body units, which must then be destroyed as well. Quads also have dark forms which are much weaker to the light beam.
Floating patrol units. Rezbits have various energy weapons as well as a directional shield which can deflect any attack. Rezbits also have the capability to completely shut down Samus's suit's systems, requiring the player to "reboot" them manually by pressing the L, R, and B buttons simultaneously. Rezbits take a lot of damage to destroy. Hence, the best way to deal with them is to quickly freeze them with a charged dark beam shot and then shatter them with a missile.
Two-legged robots that hang from and move along the ceiling. Mekenobites have powerful weapon systems, and can only be destroyed with simultaneous missile hits to each of their legs. This can only be done with the seeker missile launcher. After being hit, the mechanoid will fall to the ground and explode, requiring some distance in order to be fully avoided.
Large bipedal assault units. Ingsmashers tower over Samus and wield plasma mortars, repulsor shields, and daul wavequake generators. They can use the latter to unleash continuous shockwaves by slamming the ground with the giant orbs that they hold. Their shields can be disabled with the opposite color beam, which will stun the enemy temporarily. Ingsmashers take a lot of stopping. The most efficient way to defeat them is to disrupt their shields and quickly drop a power bomb, which will vaporize them.
Samus battles two major bosses in Sanctuary Fortress. The first is the Spider Guardian, easily the most difficult boss in the entire game, who must be defeated in order to obtain the spider ball. The second of the game's three Dark Samus battles also occurs in the fortress.