Well. Boss battles are very much a particular kind of story climax. Usually found in video games and super-hero movies. My favourite "boss battle" is in Equilibrium. There are two of them, really. The first the whole movie had been building up to and it's over very, very fast. The second was a surprise-ish and is also very fast and quite cool.
So if there muct be such things, make them follow the same rules as the rest of the game. No special immunities or super-hits or what-have-you.
Otherwise, story and game climaxes should be determined by the writing and play-flow. Each chapter would conclude based on the story points raised earlier, such as loss transmuted to healing, revenge vs redemption, hope destroyed, deception revealed or concealed.
You know, story. You an actualize this in-game through dialogue, cutscene, object/NPC interaction, ( opt to hack the file or not, opt to cut the villain's throat or not) even by letting the PC choose which corridor to walk down or which NPC to talk to.