It is easier to get SA in this mission than the previous two. Try it yourself, and see this walkthrough only as a last resort.
Entering the main compound
There are two ways, that might not work at certain difficulties. The first one is to run straight and up the stairs. Halfway up the stairs, enter sneak mode. Now sneak all the way, straight to the other stairs leading down. Be careful of the guard patrolling here, the other guards won't see you. Do not let any guard see you when still in your suit, you will be shot on sight. Halfway down the stairs, start running straight. If timed correctly, none of the guards will notice you.
The second way is to run straight to the boxes in front of you past the stairs. Don't stop running until you reach cover and don't open carry. This is probably only possible on normal difficulty, but the guard on the boat won't be alarmed enough to start shooting you. It is then simple (in 3rd person) to evade the gaze of the other guard on the other side of the boxes and continue to the small path ahead. If this doesn't work, it might work if you wait for the boat guard to start patrolling to the end of the boat and run once he can't see you, but this might not work due to the second guard moving as well.
Run to the Shivaay temple and walk into the area in front of it. There will be a guard to your right facing the other way, and a cult member disguise straight ahead. [There is another guard patrolling around the temple, but with some luck he should be out of the way when you are here.] If normal difficulty you can run, but any higher you'll have to WALK to the disguise and take it. If you want to collect a M4 machine gun, the guard standing with his back to you makes an easy target for collecting this. There are AKs, a R93 Sniper, a Deagle and ammo inside the temple.
Take the path ahead of you. You will be near a window into the main compound with a cult member patrolling in front of it. If you want to, you can sneak up behind him and strangle/sedate him to get his Uzi (concealable). Just drag his body to the window, otherwise it will be found and your Silent Assassin rating could be ruined. You may also ignore him and just walk behind him/wait until he can no longer see you climb in. He will open fire if he sees you climb through it.
While the cultist uniform will keep you relatively safe, you'll need a different disguise to get to your target. This doctor outfit can be gained from one of the three doctors in the other three operating rooms, but as these civilian units will immediately panic when you walk in, are always escorted by a nurse and there is at least one guard at every door, this is not a viable choice for Silent assassin. Fortunately, there is another disguise at the agency drop-point.
Chakran's office is marked on your map on the second floor, just walk straight to it. If you don't run, you should be fine. Now, there is a nurse in front of the office door. Stay out of her sight and wait until she goes out to the balcony. Then walk in, pick the lock and enter the office. Open the black box with the Hitman logo. Pick up the key and NVG (depending on what you do in 'killing Deewana Ji' you'll need both or you can leave the NVG). In the next room, pick up the doctor's disguise and (optional) the anesthetic. Now walk all the way to the elevator and go down to the basement, or take the northern stairs. On Normal or Expert, you can save when you are inside the elevator. Be careful around the nurses,they get more suspicious when you're wearing this disguise.
Getting your murder weapon
How does a doctor kill a patient? With a scalpel of course! And fortunately, there are two of them on the same floor as our target marked on the map. Depending on the location of the patrolling guard, you can take either. The one nearest to the elevator is in a locked room, so unless the guard happens to be (about to) patrol there, ignore the room and head for the next one. If not, break in and grab it, careful because a guard will somehow know that you are picking the lock and rush to where you are and stop you. The second room is unlocked, but there is a nurse in there. And unfortunately, she will immediately panic the moment she sees you pick up the scalpel. So sneak into the room and wait for the nurse to look away before picking up the scalpel and holster it as quickly as possible.
An alternative way to grab the scalpel is to go to the door with the middle left circulation vent. It is unlocked. Go in, climb the ladder and run to the southernmost vent. Climb down, and you will find yourself in the generator room. Toggle the generator switch and equip the NVG. Now go all the way back to the middle left vent and climb down and get out into the corridor. Ahead of you, to your left is the office marked with a !. Pick its lock now (guards won't bother you) and pick up the scalpel from the inner room.
Killing Deewana Ji
Before we take out our target, there is one last preparation to take care of: Go to the staircase next to the operation room, crouch and pick the lock of the door to the outside once your suspicion meter hits 0. You won't have the time to pick it after killing Deewana later unless you like getting shot at.
Now go to the operation room with your target; the one where the red light isn't burning. If the lights are out, stay well away from the cult members because somehow they can see in the pitch darkness and start shooting at you. If not, it won't be a problem and they'll ignore you. Equip the scalpel and go close to your target. Select "Kill Cult Leader" when it appears in the action menu, you'll have to have the scalpel equipped for this. 47 will operate on Deewana Ji either in full sight or in the dark and kill him.
The action will take longer than needed: a few seconds after you complete the objective you'll still be busy. Note that you can cut this action short by pressing the attack button the moment you kill Deewana, even with the lights on you can do this unpunished and make your way out before they even say 'Doctor, that's wrong! You're killing the patient!'.
Getting out of the main compound
Without power: Note that you cannot use the elevator if the power is out. Going back to toggle the generator again is probably not possible (I got my cover blown by the cult members every time I tried). So take one of the spiral staircases up to the second floor. On the spiral staircase, turn off NVG. There is enough light for you to see. Now, nobody will notice you because the generator is off. Also, be quick because if the cult members return before you have gone up the spiral staircase, they will blow your cover.
Now go to Chakran's office and take back the cult member disguise. This time, you aren't picking any locks, so don't worry about the nurse. Now walk out of the main entrance or climb out through that window.
A much easier way however is when the lights are still on and you already picked the lock to the outside. So once you killed your target, walk to this exit and start running the moment you close the stairways door behind you. You can run all the way to the exit now, there is enough room to circumvent the patrolling cultists here and stay in front of a sometimes occurring pursuit from the operation room if you cut short the killing scene.
Escape - and a little trap
Your exit is the same as your starting point. While climbing down the staircase near the exit, you will see Agent 17 at the bottom, shooting at you and running away. Is it impossible to kill him here, but you can peek around the door frame and have him shoot the wall instead of you. Do not follow him - if you follow him through the door, the hallway you are in will explode and all your efforts will go to waste, if the door closes before you get there it will become locked. Ignore him and go to your exit point to escape with a Silent Assassin rating.