Some battles in this game are hidden or will only trigger if you cause an alert by getting spotted by the enemies in that specific area.
I marked fights like this with an exclamation mark and printed them in bold.

• #1
  BOSS: Metal Gear Ray
  
  
• #2
  BOSS: Metal Gear Ray

• #1
  Fight with the sneaky guys in stealth camo.
  
  
• #2
  Starts with a gekko jumping in.
  
  
• #3
  BOSS: Blade Wolf
  
  
• #4
  Fight with the helicopter that chased you across the bridge.
  
  
• #5!
  After collecting the left arm and before for unlocking the door, go back to the location of the helicopter fight (#4), you'll face some gliders.
  
  
• #6
  Now you can unlock the gate (or cut the locks), the fight is in this next area will be ranked.
  
  
• #7!
  At the plaza with the farris wheel you have to trigger an alert, then the fight begins.
  
  
• #8!
  Boris contacts you via codec and asks for backup, just go to the indicated waypoint on your map.
  
  
• #9
  After cutting through a metal gate you have to fight some dwarf gekkos and soldiers.
  
  
• #10
  BOSS: Mistral

• #1
  Starts with a mastiff (gorilla) jumping at you.
  
  
• #2
  After cutting a metal gate and jumping down a hole you’ll face some dwarf gekkos and two soldiers.
  
  
• #3
  Fight with the three raptors after the cutscene where you save George.
  
  
• #4!
  Boris calls you for backup.
  
  
• #5!
  The guys patrolling in front of the brain room.
  
  
• #6
  The fight right after the cutscene with the brains.
  
  
• #7
  The part where you control the gekko is ranked.
  
  
• #8
  BOSS: GRAD

• #1
  Fight with the attacking cops at the beginning.
  
  
• #2
  Fight with the 2 GRADs.
  
  
• #3!
  After clearing the area of enemies Boris calls you for backup.
  
  
• #4
  The fight starts with gekkos jumping through the office windows.
  
  
• #5
  Fight before you can enter the elevator.
  
  
• #6
  After jumping from the crane to the next building, jump again to another building and head to the left, there is a hidden blue box. Leave the area and the fight starts.
  
  
• #7
  A heavily armed cyborg (the ones with the hamer) jumps in, more enemies will join the party.
  
  
• #8!
  Trigger an alert at the roof where the 2 soldiers are, a helicopter will appear.
  
  
• #9!
  At the end of the dark tunnel is a platform with 2 gorillas and some dwarf gekkos, trigger an alert to get ranked.
  
  
• #10
  After leaving the tunnel you have to fight some soldiers and a GRAD.
  
  
• #11
  Soldiers and gorillas patrolling on some stairs.
  
  
• #12
  Fight at the plaza where you can hear the surpressed thoughts of the soldiers.
  
  
• #13!
  After getting screwed up by the last fight, kill all the soldiers in the next area with your new awesome ninja moves (aka drunk mode).
  
  
• #14
  BOSS: Monsoon

• #1
  First Lobby fight.
  
  
• #2
  When the doc is done hacking the elevator stay in that area and fight till a GRAD appears. Kill it and you’ll get a ranking.
  
  
• #3!
  Get caught at the area where you have to cut the three panels.
  
  
• #4
  The part where you have to ninja run through the building.
  
  
• #5
  First fight in the japanese garden.
  
  
• #6
  Elevator fight #1
  
  
• #7
  Elevator fight #2
  
  
• #8
  Elevator fight #3
  
  
• #9
  Elevator fight #4 (after jumping to the second platform)
  
  
• #10
  BOSS: Mistral and Monsoon AI.
  
  
• #11!
  After the cutscene with sundowner go back to the room where you fought the AI’s to trigger this fight.
  
  
• #12
  BOSS: Sundowner

• #1
  Right after the cutscene you'll get spotted by soldiers.
  
  
• #2
  Fight at the plaza.
  
  
• #3!
  Trigger an alert at the stairs to get a ranking.
  
  
• #4!
  After Wolf contacts you via codec, you'll have to fight some guys in that next area. Then use your AR vision to spot a soldier behind a metal gate, enter the building and head to the VR terminal. The fight starts when you try to leave the area.

• #1
  BOSS: Turbocharged Tobias

• #1!
  The soldiers patrolling in front of the gate.
  
  
• #2
  BOSS: Metal Gear Excelsus
  
  
• #3
  BOSS: Senator Armstrong

I hope this guide will help you getting your Stormbringer, good luck and have fun!