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This mission is probably the easiest out of all of them, but regardless there are a few things that will make life much easier for a stealth approach. This guide explains how to rescue emily non-lethally and undetected.
First the best entrance to the lighthouse is through the sewers which are located to the far right of the right entrance.
There are a few guards in the area, but most of them will have their back turned to you so they shouldn't be a problem. The next difficult area is when you get close to the elevator.
Teleport to the lower platform. Then turn around and you can teleport to a higher slab of concrete.
Then teleport to the roof above the guards. From there teleport as close as you can get to the guard standing near the elevator. Sneak up to him and take him out.
At the top of the elevator all the guards are very easy to take out. After you get to the top area you can take out Hamerlock, but I chose not to. The best entrance to that area is over the roof, you will be able to drop down from above to eliminate hamerlock. After you rescue emily the game is over.