Samus fights the Spider Guardian in the Sanctuary Fortress. The Spider Guardian does not actively attack Samus, and instead moves along an extensive, labyrinthine Spider Ball Track while shielding itself with a damaging magnetic field. Morph Ball Bombs merely weaken its shield, and it can only be damaged by forcing it to collide with electric fences. To do this, Samus must weaken the Spider Guardian's shield until it turns green, then activate the Bomb Slots in the correct order so that an electric fence is turned on and the Spider Guardian's path is directed towards it.
"This darkling Pillbug has absorbed the power of the Spider Ball. It can travel over magnetically charged surfaces at will. The creature seems to have a connection to the local energy system. Aggravating it may cause disruptions to the system."
The Spider Guardian boss battle is infamous for its high difficulty level, generally considered to be one of the most difficult bosses in the game. Multiple reasons for this exist: the large distance from the Save Station, the great amount of damage the charged "aura" can deal to Samus upon contact, a limited amount of energy recharging, the sometimes unpredictable patterns the boss moves in the last phase (with a tendency to get in the way), and the need to do precise Bomb Jumps within a very tight time limit in the last part of the fight. The fight's difficulty was heavily toned down in Wii versions of the game, partially due to the Spring Ball.
The Spider Guardian is one of only two bosses in the Metroid series that is "fought" in Morph Ball mode alone, the other being the Caretaker Class Drone. Both are from Echoes.
The Spider Guardian's aura strongly resembles that of the Death Ball.
The Spider Guardian can only be scanned prior to the battle, since Samus cannot come out of the Morph Ball mode once the battle begins. She can scan it while it runs along a Spider Ball Track through a window or by the hole in the room prior to the fight. It is one of three Metroid Prime Trilogy bosses to have this distinction (scannable prior to the actual battle), with the others being fellow Echoes boss Alpha Blogg and the Omega Pirate in Metroid Prime.
If Samus attempts to exit the fight with the Spider Guardian by going through where she entered the battle, and opens the door, the game will crash.
In the Wii versions of the game, the Zoom function present in the fight (the only time such a function is featured) is removed, and the fight now takes place entirely in full screen, with the Letterbox removed.
In the demo, the Spider Guardian was called Spiderling.