Final battle There are two types of the final battle with Muro. You can influence how the final battle will look like in the 14th mission (TCTF Redux). In the last room, with Griffin and Shinatama, first shut down Shinatama and after the short sequence, where Griffin shoots Shinatama you can either kill him, or leave him be. If you leave him alive, he will arrive with a helicopter and two TCTF special agents and help you against Muro and his men. However, if you kill Griffin you will have to face Muro alone. He won't have any help either, but the Crysalis will evolve him into the Imago stage. In my opinion the Mutated Muro is fairly easy to defeat, once you find a strategy, on the other hand the fight with normal Muro is much more exciting, with his men and the TCTF squad interfering.
Items

You can pick all kind of usefull stuff lying around in Oni. In this sections are some tips on the less obvious locations that contain bonus items and some hints to make the game easier for you.

 
Regional TCTF (Counterattack) After you kill the striker standing on the armoured van that broke through the front of the building, try to jump on the van. You can also jump on it from the bridge on the second floor. A hypo and a energy cell will be your reward. (as well as a plasma gun if you're fast enough)
  Try to save your TCTF colleagues. They will help you in return and some will even give you hypos and ammo.
  In the room where Barabas kidnaps Shinatama shoot both windows. On the ledges are some goodies. Just watch out when you are taking them, the ledges are slippery.
Conversion center (Interior) There is a superball gun hidden on the left machine at the start.
  When Shinatama is about to explode a grunt will appear on the stairway. Kill him for two additional hypos, but be quick and watch out for the Xios explosion.
  Inside the room with the acid pools and electricity going trough the walkway is a shield between two platforms. You have to jump into a crack in the wall and then you can jump on the platform with the shield.
Rooftops There is a hypo behind the last machine near the place where you see Mukade jumping on a higher ledge and running to the elevators. There is a energy cell if you look around the glass elevator.
  After going up with the elevators and jumping to the roof on the right, jump on the upper walkway. Here you can take two hypos, each on one side and a shield, when you jump from the end of the walkway on the machine
  Just before Save 3, you can jump onto a ledge to the right under a roof. You have to make your way under the roof, by jumping over the girders. There is a Hypo on a lower ledge and a Ninja guarding a Superball Gun at the end. Just watch your step. The fall is long.
  You can return (if you wish) from the end of the rooftops (just before you enter the lift that takes you to Mukade) to the very start. If you have been killed, all the items will respawn including the ones that are in the previous parts of the rooftops.
Regional TCTF (Redux) In the room where Shinatama used to sit shoot the windows on the left and right, on the balcony is a security guard with a mercury bow.
Syndicate compound Search the outer compund completely, you can find an invisibility just behind the boxes at the start, a hypo behind the tower on the right, another hypo in the first small hangar, ballistic ammo behind the helicopter another hypo behind some boxes on the opposite side near the tower. A energy cell near a container to the right from the doors leading inside and a Superball gun, a phase gun and invisibility even further to the right. Additional bonuses in each tower: hypo, balistic ammo and shield/invisibility. The only question is how to get inside the towers? Weell.. that's also possible without cheating.. When you survive the snipers enter the building. Then go to the only alarm console. Jump on top of it, then run and jump-roll on the bookcase on the left.Position your camera so you look from under Konoko and do a Jump-roll. Voila.. you're on the roof. After that it's easy to jump into the Tower and collect the goodies.
  When you break through the door with the armored truck, there is a hypo to the right, behind a machine. Also when you are on the first floor enter the right door first, you'll fight a female striker that will drop two shields and a hypo. If you then go out of this small room and to the right you'll see a invisibility on a ledge in the corner.