Unlike the previous two missions, Shogun Showdown is a fun and proper level where you'll get to sneak around and fool security the way Hitman should be.
Getting a disguise and weapon
This is the tough part - getting the Night Ops ninja disguise (black ninja uniform) without any alerts or kills. At the beginning, don't go up the stairs on your left - you will with absolute certainly get spotted and probably also be killed! Instead, look for the secret door at your front-left when starting.
Walk up the stairs (if you run, the guards will come after you [on difficulty higher than normal]) and look through the keyhole. A Night Ops ninja will be patrolling in front of you. The moment he turns his back, open the door and walk left along the support beams - DO NOT STEP ON WOODEN FLOORBOARDS. Then turn right towards the stairs. Wait behind the pillar until the patrolling guard is behind another pillar. Or, if you're not going for Silent assassin, shoot him in the back of the head with a silenced gun and take his uniform. Still walk over the support beams because the creaking will alert the two guards behind the laser grid.
Drop down the stairs and walk to another hidden door to your right. Run along the passage and wait in front of the door. A CWC ninja (white camo ninja uniform) sometimes comes to meditate. Let him leave and enter in sneak mode. Pick up the keycard on the shelf to your right and continue on ahead. This leads to two identical obstacles of patrolling guards going circles while a ninja lurks in the rafters. Remain unseen by the patrolling guard (easy considering the lay-out) and hug the wall and crouch to get past the ninja. Follow the exact same procedure the second time around.
You're now in an abandoned hallway. Go to the third door to your left (so around the corner). Sneak, open it and take the uniform nearby. Get back before the two ninjas watching TV spot you. Go to the room over, there is an area cordoned off with a laser. Deactivate the laser (keycard is needed for this) and enter. Pick up the SMG-SD6 if you don't have it and the bomb and remote (for Bomberman - see below).
Pick up the guidance system
Go back all the way to the room with wooden floorboards. Walk to the laser grid, deactivate it and go right. NOTE: If a guard checks your ID your cover will be blown, so just walk by them and ignore their hand-gestures. There is a staircase going down. Take the staircase, cross the basement diagonally and go down to the museum. If you take the door to your right in the basement, you'll encounter a ninja guarding the laser grid. Not necessarily a problem, but better avoided considering how easy it is to take the other entrance. Deactivate the laser and pick up the guidance system, the .22 SD and the katana (if you want it). You get a bonus save here.
Return to the 1st floor.
There are two methods:
Approach 1 : Bomberman
Go down to the helicopter and place the bomb on it. Then go to the 3rd floor, dodge the guards and press the button. Hayamoto will be alarmed and will try to escape by the helicopter. Blow up the bomb at the correct time and walk to your exit. You can do this by either waiting near the exit and checking your map or watching from the wooden rafters you get on after climbing through the window of Hayamoto's room, giving you an undisturbed view of the scene. Wait for the chopper to get high enough to not alert any guards with the explosion (Roughly when the chopper finished ascending and starts to leave.)
Approach 1.2 : Bomberman
While at the museum, drop the bomb somewhere Hayamoto won't see it before getting in detonation range. He'll enter the museum through the unguarded gate, walk to the middle of the room and then in between the two pillars, so behind the pillar in between the guidance system and the .22 would be the best place to place it.
After pressing the button (as described in approach 1), use the map to keep track of him (so practically impossible strategy on Professional) and blow him up when he gets in range. This is a much smaller time window than the chopper so not really advised.
Approach 2: Close and personal
After being alarmed because you pressed the button, Hayamoto will first go to the museum to pick up his precious guidance system before evacuating to the chopper. Taking him down on the way down can be done if you hide in the concubine's room and shoot him while he descends the stairs, but this will never remain unnoticed. There is one window of opportunity to catch him unguarded however, at the museum.
On his way down, the guards will run and take strategic positions to safeguard Hayamoto. And they will see through your disguise right away. They won't go into the museum though, and you can run there without raising too much suspicion before encountering them. Wait for Hayamoto there, hiding behind the pillars. It is possible, though difficult, to strangle him. Or just shoot him with a silenced gun, although the elite guards might hear this. Not picking up the guidance system before this might give you a larger window of opportunity.
Getting out unseen will be difficult however, and will probably not work while getting a Silent assassin rating.
Approach 3 : Classic 47
You won't need the bomb. Go straight up to the 4th floor and enter Mei Ling's room. She gives you the special keycard and you get a bonus save. Now wait under the stairs until the concubine comes down, don't be seen because she will instantly recognise you from any distance. Avoid or sedate her and go to the 5th floor. From now, only sneak until you kill Hayamoto. Get in and go from the left. The ninjas in the rafters are cool with you, it's only the ninja with a gun that causes trouble, so keep out of his sight as you sneak up the stairs.
If timed correctly, Hayamoto will be standing in front of the window. Sneak up behind him and fiber wire him. [Note: if the gun ninja comes up to check your ID, sedate him without anyone else seeing. It is difficult but doable.] Now exit through the window as fast as you can or the ninjas will cut you down.
The easiest escape is : forget Mei Ling. (You rescued her from Lee Hong in the previous game, so why did she get herself into trouble again? Let her suffer for once) Leaving her after she gave you her special card does not harm your stealth rating. There is a path outside the window that apparently leads to only Mei Ling's room. But drop off the next to last ledge and you will find another path to the left that will drop you directly in the courtyard, one you cannot take if you enter Ling's room. Let the ninjas run around inside the whole compound. With total swag, walk up to the helicopter and escape in style. (The stupid guards will point their guns at the chopper, but that's just about it) This got me the Silent Assassin rating.
Silent assassin rating (alternative description)
This is actually a pretty fun level with various ways to complete it, unlike the previous two levels. The description beneath will kill no-one but Hayamoto Sr., but if you do decide to kill any guards (in the stairs region of the map) you'll have to drag them all the way to the starting point if you want to be sure they'll never be found. While there are various passageways and empty rooms without people patrolling, people will find the body after the alarms go off and the guards deviate from their routes.
-Go though the door right in front of you. Walk instead of run to avoid being seen by guards outside. You'll enter a room where 47's comment about the creaky castle will make sense; the floorboards creak here. If you walk over them, the guard patrolling and the two guards behind the laser grid will be alarmed. Stick to the solid wooden beams running over the floor and next to the pillars.
-Sneak to the stairs down. You'll now enter the living residences of the guards. There is a guard who will regularly meditate here, allowing you to sedate/strangle him, but wait for him to leave and sneak by instead. Do take the keycard on the shelf to your right though.
-Sneak through the hallways. There will be guards patrolling, but as they are going circles it is child's play to sneak around them, be wary of the ninja's in the support beams though. Sneak all the way to the south room with the ! and go to the east door of the room to its right instead. You will find a guard uniform here, put it on before the two guards in the room spot you.
-Go to the room with the ! now. You can run in normal mode, but with harder difficulty you best walk to avoid them following you. Grab the bomb and the remote detonator and leave again. With your new uniform, you can now move through the courtyard to the chopper, walk to avoid suspicion. When no one can see you, plant the bomb. Unlike the car bombs, you'll have to detonate this bomb manually but that will be a while still.
-Head up the stairs to the guarded laser grid in the creaky room and go downstairs there. One floor down, take the door opposite to you rather than the one next to you and enter the museum. You can grab a katana and a .22SD here, and the guidance system. If you couldn't plant the bomb or just want to make an escape in the helicopter, you could always just drop the bomb near the guidance system's pedestal instead. When Hayamoto is alarmed, he'll always go here before escaping first and he'll go alone so no collateral damage.
-Go up the stairs again, you can pick up another katana on the second floor if you didn't in the museum, and go to the third floor. From this point on there are multiple ways to go about it. The most Silent assassin approach would be to go to the ! on the map; the security system. Press the big red button to trigger the alarm, this will urge Hayamoto to flee.
-Optionally, go to the fourth floor and talk to Mei Ling in the right room. Do not be seen by the concubine patrolling between the sixth floor and the room on the left, she will immediately panic and alert the guards regardless of how far away you are when seen (version 1.0). Be sure not to be seen by Hayamoto or his ninja's while they descent the stairs either, they too will recognize you and attack. Mei Ling will ask you to take her with you and give you a special keycard and an additional save. This is not advised for silent assassin though, as she won't come with you until Hayamoto is dead and will therefore make getting out unseen extra difficult. Leaving her after getting her card does not harm your stealth rating.
-Go to the exit or the chopper (if bomb in museum) and wait for Hayamoto to get within range of the blast. You can go to the exit through the stairs if you can run faster than his personal guards, or you can take Mei Ling's keycard and go upstairs to take the escape route outside his window. If you take this scenic route, you can watch Hayamoto get into the chopper but the map will do fine too. This is useful because if you wait long enough for the chopper to get high enough none of the guards will be alarmed by his death. You can then follow the path to the exit.
-Another option is much more aggressive but can still work: Go to Mei Ling and get the special keycard from her. Go to the sixth floor, it might be easier to go down a floor and take the northern stairs instead of the southern to avoid the concubine.
-Enter Hayamoto's room and strangle him while he's looking out of the window. This might be very difficult as you'll need to evade his line of sight completely but have do it before the concubine returns to see you, and the ninja's above or the guards downstairs might get suspicious as well.
-Climb through the window and follow the path to Mei Ling's room, walk to her and run to the stairs the moment she'll follow you. Run past the aggressive guards to the exit, somehow you'll still be able to get a silent assassin rating this way.