Here is some basic information about this final battle:
First of all do not think about this battle as a traditional boss fight, because you will not have to defeat any tough opponent in direct combat. Melee fight are possible in later phase of the battle, but can be avoided. Even if you get to this point, they will be easy to win.
Second of all, you have a great freedom about choices of your tactics. So you do not have to worry about winning this battle, even if your character specializes in remaining in hiding.
Also the important news is that during a battle you can save the game. But his can only happen if you are not attacked by anyone.
Map legend: 1 - Switch off supporting system terminal; 2 - Zhao Run Yu; 3 - Human modules; 4 - Computer terminals; 5 - Storage rooms.
Before we continue with the battle, first a few words about the room where the Hyron Project is located. Absolute priority in this battle is to avoid defensive turrets hung on a rotating structure #1. They move in a circle and shoot any target in their field of sight. The most effective way to avoid them is to use a camouflage and hide behind covers. You can also destroy turrets. I do not recommend using EMP grenades, while turrets are not on the ground. It is much better to use good weapons and particularly effective in this case is a plasma rifle #2. It is worth noting, that destroying all turrets will not result in any negative consequences (e.g. another security systems to be activated).
If you run out of ammo during the battle, then you might use two storage rooms located at the very bottom (Storage A and Storage B) #1 #2. Unfortunately, in order to reach them, you have to get close to the center of the room. Besides that, storage rooms are not available from the beginning but later. Inside each of the storage rooms you'll find weapons, ammo, grenades, medical supplies and battery charging stuff.
There are also few destroyable walls #1 on the outskirts of this room. If you have the Punch Through Wall augmentations, you should consider breaking them, because you'll get good covers thanks to that #1. You can also use these places as shooting points.
Definitely fastest way to win the battle is to get to the central construction of this room #1. Remember about previous warnings and either use a camouflage (the Glass-Shield Cloaking System augmentation) or destroy defensive turrets. Explore the south-western part of the central construction, finding a control terminal, attached to the wall #2.
A mentioned terminal has highest, fifth security level lock, but you can also use a code 2012 #1, obtained from Hugh Darrow as a reward for successful negotiations (you'll find more info on this in a description of Step 3. After logging into the system, decide to switch of the supporting system #2.
Thanks to that you'll skip a large part of the battle and you'll be able to focus on attacking Zhao Run Yu #1. It is best to use a rocket launcher or a laser rifle #2 to inflict her damage. She won't be able to defend herself, but if you haven't destroyed defensive turrets yet, then you need to use a camouflage (the Glass-Shield Cloaking System augmentation) or attack Zhao from behind a good cover.
An alternative method is to fight the entire battle. In this case your first task is to destroy three human modules marked by the game. Before you can destroy a module, you have to open it and this can be done in two ways. First option is to get down in order getting close to the central construction #1. Remember about previous warnings, so either use a camouflage (the Glass-Shield Cloaking System augmentation) or destroy defensive turrets. After reaching the central construction, find a button near a human module #2 and press it.
A second option to open modules is to interact with computer terminals on the outskirts of this room #1. If you haven't destroyed defensive turrets, you have to hurry with interacting with terminals, because the glass which separates you from them won't stand too long their fire. A solution to this problem is to use camouflage (the Glass-Shield Cloaking System augmentation) #2, but you would need a big supply of batteries.
Each of mentioned terminals has fourth security level lock, but you can use password from previously found PDAs #1. These are iwntlove (login hualing), frgottn (login daiyu) and yyyyyy (login marilyn). After logging into the system, each time quickly select opening door option #2.
In both cases (using buttons or computer terminals), your goal is the same - opening the module. Once you're succeed, start attacking the person attached to the machine and do not stop shooting, regardless if you're attacking it from a long #2 or a short #2 distance. I suggest using good weapons here, so you can make sure to kill the person and destroy the module before it closes again.
With opening the second module, things get complicated, because a group of insane guards will appear in the area #1. The easiest way is to shoot them. But if you're a pacifist, the use a paralyzing weapon on them (do not let them see you!) or deal with them in a melee combat #2. In the latter case you can't let them surround you.
After destroying all three modules, a second phase of the battle begins. You'll recognize it, because Zhao will surround herself with a glass barrier (screen above).
Zhao won't fight you directly, but defend herself by creating electric discharges in particular sections of this room #1. If your character has the EMP Shielding augmentations, then you can ignore these attacks. Otherwise you must avoid them at all costs and the best places to hide are previously mentioned storage rooms #2.
Discharges are not your only problem, because hostile robots will also appear in the room #1. You can defend yourself in lower storage rooms or somewhere on upper platforms, using EMP grenades #2, Typhoon ammo or good weapons to blow them up.
If you have the EMP Shielding augmentation, then you can start attacking Zhao after destroying three human modules #1. Ignore electric discharges and do not wait for a first robot to appear (you can use any cover to hide from it). If you do not have the EMP Shielding augmentation, then you have to defend yourself until you destroy all robots. It will make further discharges to disappear and Zhao Run Yu won't be defended by a glass wall anymore #2. In both cases use a rocket launcher or a laser rifle to attack Zhao, and after few seconds you'll win.
Regardless of your tactics, you have to attack Zhao Run Yu until you kill her (screen above). Scroll down not to the Endings section of this guide.
Reward: 1000 experience points.