The layout of X16 is alot more straightforward and linear than the last lab you visited, however this one is filled with both zombie stalkers and Snorks but you should be more or less used to them by now. Your starting point is the eastern side of the lab and the your main goals, along with the exit, is on the far western side.
Sakharov inside X16.
Move down the stairs (be mindful of the Burner anomaly), dispose of the two zombies in the room ahead and move on. Go down the ladders. When you're on the bottom floor you'll find yourself in a large room - there are more enemies ahead... yeah, more zombified stalkers and a Snork. Deal with them and move on. The area doesn't really have anything interesting in it.
You'll soon come to a room with an alcove to the south-west and with more zombies and another Snork in it; once you've dealt with them be sure to break all the boxes in the alcove since one of them contains some 9x39 mm SP-6 rounds. Moving north you'll find another room with alot of shelves in it - you can find a number of metal boxes on them - be sure to check them all since they'll turn up more 9x39 mm ammo and some other goodies.
Beyond the room, and after having disposed of more Snorks you'll come to a large, circular room - consider creating a new savegame before you move in. Once you do, the timer (as hinted by Sakharov) will start and you'll have a few minutes to close down the machine. The circular room consist of a number of different levels - each of them has a switch on it (marked on your map), and you must activate them all to turn off the psi-emissions. You may also notice that your minimap has detected a number of PDA's nearby - don't worry (too much) since these are all in fact more zombies.
On your way through the room be sure to be on the lookout for anomalies, artifacts (there's a bundle about), items, and of course enemies. You don't have to pick up everything at first since you can explore the room once you've turned off the emissions, so stick to that objective if you run low on time. The final switch is all the way at the top.
Notable items, beyond the large number of artifacts, includes a Berill-5M Armored Suit and close by a crate with a SSP-99 Ecologist suit in it; since you're probably pretty much loaded I would recommend ignoring the latter, although the first armor may be worth dragging along.
When you finally turn off the psi-emitter you'll pass out (again) and be treated to another cutscene. Hmm, this Strelok fella' sure was keen on getting to the center of the Zone, Chernobyl specifically.
Ghost on X16
You next mission is to pick up the documents and get out of the lab. Move towards the west and you'll soon come to another large room - it has a Controller inside so deal with it first and enter the room. Inside you'll discover a body: it's Ghost - search him and you'll get some more information from his PDA, including a recording shedding some more light on what happened. Ghost seems to have met his demise at the hands of the controller, and it sounds like this "Doc" character will know where to find Strelok. You'll be given a new semi-optional mission, namely Meet the Guide. Be sure to pick up the documents from his corpse along with the Ghost Suit if you wish (this is the suit that Sakharov is looking for).
As you may have notice I called Meet the Guide semi-optional - it is an optional mission in the sense that you don't have to complete it, but for you to fully explore the plot and gain access to the "best" endings of the game, you must complete it.
Although the arrow on your minimap may seem to indicate that you should backtrack towards where you initially started out, you actually need to drop down a hole close to where you discovered Ghost; it's inside one of the "cells" with a sign (saying "10") in front of it. Before you move on, though, you may wish to search the room thoroughly - you can find some boxes, one of which contains a M209 grenade. Before you drop down make sure that you have everything with you that you wish to bring along, because once you drop down there you're not likely to come back.
When you drop down move towards the east and you'll come upon another hole and some metal boxes nearby - be sure to break these as they contain a number of goodies, including the still rare 9x39 mm ammunition. Head down the next hole and you'll come to a level transition. Once loaded, you'll find yourself back in Yantar - well, some tunnels beneath the area, to be exact.
I'm sure you'll be thrilled to hear that the tunnel not only has zombie stalkers and Snorks in them, but also a Pseudogiant. You'll hear what appears to be gunfire and explosions - you'll soon find out that it's in fact military choppers that has been sent in to deal with the zombie stalkers. Finally some justice for the little guy... or something.
Getting out of the underground should be pretty straightforwards since, for the most part, the tunnel is going in one direction; at one point you'll find the tunnel splitting, going both south and east; take the one going south since the one going east is just a slight detour with nothing of interest along the way and you'll end up in the same place anyways. This particular area has the Pseduogiant near, so watch out.
Sakharov outside X16.
Eventually you'll come to a broken grate and beyond that a ladder going up. Head up and you'll find yourself in Yantar proper again; go up the stairs and look for the broken rail - jump down from that onto the fence and the other side.
Go and talk to Sakharov who will basically thank you for turning off the psi-emissions. Strangely, he'll give you an optional mission: Purge the lair of the snorks; the reward for this mission is 3000 RU and two scientific first aid kits, so if you need some cash feel free to do it. Notice that Sakharov now has a wider assortment of equipment available, including the Tunder S14 assault rifle, the SEVA Suit, and 9x39 mm PAB-9 rounds. He may not have all the items when you visit him since his inventory seems to be randomly generated each time you enter the area - so you can always try to head into the Wild Territory and come back to check his inventory. If you decided to pick up the Bring the unique bodysuit (or you pick it up now) you can give the Ghost Suit to Sakharov; he'll reward you with a SSP-99M Suit, the armor with the highest protection average in the game - in other words a pretty good armor.
You're not going to come back to Yantar unless you need to buy equipment from Sakharov or possibly to complete an optional mission - in any case, you should bring as much loot as you can carry with you back to your central stash at the Bar since your next destinations are going to be the Army Warehouses and beyond.
Once you're back at the 100 Rads deliver the documents to the Barkeep. Although he says that the psi-protection prototype you're carrying wont protect you forever, and that you should hurry to the Brain Scorcher, you can actually take all the time you need.
The Duty HQ is located to the north-east of the 100 Rads. There is a control point just outside it, but if you talk to the guards there you can tell them that the Barkeep sent you, and they'll let you pass.
Inside the HQ you can find General Voronin. Talk to him and he'll explain how Duty basically is at war with the Freedom faction. He wants you to steal a weapon from them, namely a Bulldog 6 grenade launcher. Don't worry if you wish to be on good standings with Freedom because you can complete this mission without having to steal it from Freedom. While you are here, also be sure to pick up another mission - Find the enhanced rifle. If you complete most if not all of the optional missions for Voronin you're like to become friends with Duty. Sadly though, this doesn't mean you can join the faction. It does mean that Petrenko (see below) will sell a wider selection of equipment - nowhere near as impressive equipment as Skinflint, though.
You may also wish to pick up the mission to kill a stalker called Vampire, although this will take you back into Dark Valley. The mission is likely to net you two unique weapons, the Noiseless Viper and Sniper Obokan (as loot you find) and you'll get a Fireball as a reward for completing it.
Just south of the HQ you can find Colonel Petrenko who can also provide an optional mission - he wants you to kill a stalker from the Freedom faction; since this isn't going to be popular with Freedom you should only pick up this mission if you don't care about them being your enemies. This mission ties in well with a mission you can pick up at the Army Warehouses, so you may wish to wait to pick up the mission until you're ready to move into that area. Petrenko will reward you with a PSZ-9Md Universal Protection suit.
Although you can complete these missions later I thought I might as well explain them now. They're both fairly simple and quick to complete. Guide is located in Cordon, the same place where you met Fox. When you get there, he'll basically tell you that the Doctor, who you are now looking for, can found in Streloks hiding place - in other words at Streloks stash in the Agroprom Underground. You'll get a new mission: Meet with Doctor. Head to Garbage and into Agroprom Research Institute. Getting there should be pretty straightforward.
Ok, Doc refers to you as Strelok... which must mean that... ok, ok, apparently your primary mission is to find and kill yourself. An easy task, I guess, and the game will in fact end if you kill yourself - however not really in a satisfactory way. There must be more to the story - I reckon that the stash at Pripyat, that Doc mentions, must be worth checking out. You'll be given the semi-optional mission Stash at Pripyat (again, semi-optional because you need to do this mission to gain access to the best endings the game has to offer).