Straight from one of the guides from GameFAQs by CyricZ.
This is more of a puzzle boss than a flat-out fight boss, and it's fought
entirely in Morph Ball form. So, this Pillbug has your Spider Ball, and it
will use it to roll around on Spider Tracks. It can only harm you by making
contact with you, but its entire colored halo is considered "contact", and
it can hit you through walls if you're close enough. What you have to do is
to bomb it so that it turns from blue to red to green. Once it turns green,
a Bomb Slot will be open to you. Activate the Bomb Slot to open a path to
an energy conduit, which will damage the Spider Guardian. That's it,
really, but it does get pretty complicated. The first area is a simple
rectangle with branching passages. Try to stay near the top so that you're
close enough to the Bomb Slot to get there in enough time. Once that's
done, you'll move on to a Boost half-pipe. I suggest staying on the upper
right side and wait until it gets close and dropping down the halfpipe,
laying Bombs in your wake, OR getting on top by going up the left side and
falling down the middle hole dropping Bombs in its path. Once it turns
green, a small platform will extend below the Bomb Slot so you can get there
from the top. The third area is slightly more complicated, but mostly in
the path the Guardian travels. You can still Boost to the top and drop
Bombs on his path, then, once again, turning him green creates paths for
you to travel on to get to the Bomb Slot. Get him here and you'll move on,
get to some supply crates for the hurting you're probably feeling, and
you move on to the final area. This area has three energy conduits, and
he'll have to hit all three. This area's tough, because there are few
places to hide, so you're gonna take lots of damage, here. I suggest
sitting near the opening in the middle of his path, then laying a few Bombs
as he draws close, with enough time for you to get away, but also leaving
space for the Bombs to hit him. You need to sit above the recessed spots
in his path to avoid damage entirely. Anyway, when you get him green, use
the Bomb Slot on your left on the second level, but only when he's to the
right of the moving panel so he rolls up instead of into the panel. Once
you hit the first one, you'll need to get him green, then bomb two Bomb
Slots, one in the upper right corner of the area, then the one in the lower
left. Use the Boost to carry yourself across small gaps to save time.
Once he hits the second conduit, you need to get him to the third and most
difficult conduit. You positively must turn him green as he's travelling
to the right about midway through the tunnel, or this won't work. You need
to move fast and energize three Bomb Slots, one new one in the upper left
corner of the room, then the other two in order down. If you pull it off,
the Guardian should just be in position to roll right to its doom. Alan
MacDougall has dropped me a good hint for fighting him. Once you bomb it,
his force field will disappear for a moment, so you can use that to roll
right by him if you need to avoid some damage.
Hope this helps.
