Chapter 3. FOREST OF SUKNASARI. At the very end, after you untie the airship, there will be a boss battle.
Chapter 5. CHAMATKARI MANDYR. The first battle with Vincent.
Chapter 9. ANATOLIA. A new boss appears here (associated with him is the achievement "This is tin"). You can't move into this GEARHEAD boss either. He will be caught several times throughout the level.
Chapter 11. DOSUDEN. There are also GEARHEAD battles and a boss battle from Chapter 3 at the end of the level.
Chapter 12. PESHANDEN. There are also battles with GEARHEAD and, at the end, a fight with Vincent in the very crease.

In all meetings with bosses, you have to try to get into them. Chapters can be played in any convenient order.