The second time you see the SA-X is in sector 2, TRO. The layout should be familiar- there is a long hallway with a long horizonatal beam dividing the two areas. The SA-X is on the bottom half, and is walking to the door on the far left. Normally, you sit on the top area, watch the SA-X go through the door, then bomb the far right blocks and go through it yourself.
All you have to do is get through that door first.
Now, getting through the door is hard enough, but if you really wan't a challenge, try doing it without taking any damage- you will need flawless timing and great morph Ball jumping skills.
And yes, I did this earlier, so I know it works...
K, did it.
Really now, did you?
How could you possilby have gotten to that point and finished it, without damage, in less than an hour?