Sigma is back, Zero is gone, and X is left all by himself to fight off the Mavericks. Not long after X starts his battle against Sigma's associates, he finds out that Zero's parts are still intact and that Zero's memory chip is still in the computers with Dr. Cain. Zero's parts are divided up into three parts. Each part is held by a group of special Mavericks called "X Hunters". Violen, Surges, and Agile challenge X to defeat them and retrieve his buddy's parts.
Much Like Mega Man X, there is more than one way to fight through the bosses of the game. I prefer the weapon weakness method because you get to see certain enemies die differently when you kill them with their weakness.
The order of bosses by weapon weakness:
   1. Overdrive Ostrich
   2. Wire Sponge
   3. Wheel Gator
   4. Bubble Crab
   5. Flame Stag
   6. Morph Moth
   7. Magna Centipede
   8. Crystal Snail
     This is a different method through the bosses that I recomend for inexperianced Mega Man X players. Overdrive Ostrich is a little hard so early in the game unless you know his attacks very well and are really quick with the controls. I recomend that you fight Wire Sponge, Wheel Gator, and Bubble Crab first so that you have a few Heart Pieces and Sub Tanks to fight Ostrich with.
Recomended order of bosses method:
   1. Wire Sponge
   2. Wheel Gator
   3. Bubble Crab
   4. Overdrive Ostrich
   5. Flame Stag
   6. Morph Moth
   7. Magna Centipede
   8. Crystal Snail