Some tricks I have found after playing through five different ways

I have played through on five different ways, and each way revealed some interesting hints.

When you have intel to sell, you can sell it to Hallbech, the black market or send it to scarlet.

Scarlet wont give you as much money as the other two but it ups your rep with her when you do send it to her.

Certain people will pay you not to kill them. Nasiri, Brayko, and Shaheed.

Some people will give you special guns if you kill them. Oemn Dang gives you a shotgun, Brayko gives you gold smgs, Shaheeds general give you a gold ak47 and Marburg gives you an excellent pistol. So basically you can end up with special guns for each slot. The guns are worth a lot on the black market if you sell them.

Buying the map to marburgs villa will reveal a secret door in the garden right before you escape. Inside is more intel on alpha protocol that will help you expand your dossier

Dont kill sis on the yacht, her handler is the leader of g22 Albatross. He will help you in future missions if you spare her and form an alliance with him, but dont tell him about the locket sis gives you or he will get mad.

Sie likes to be attacked and talked to aggresively in order to increase your rep with her.

Madison likes to be reassured, Mina likes to be treated proffesionally, steven heck likes you to talk a big game, albatross and marburg like you to be stealthy, Shaheed doesnt care what you do as long as you dont kill him.

In taipei you meet Hong Shi. He likes to be respected. Once you get dirt on him you can either use it to show loyalty, which causes him to back you up in future missions, or blackmail him for money.

The less people you execute during cut scenes with dialogue, the more intel you get, and sometimes money from them.

Go through Darcy's training, then when he asks you to run it again, say no. He will ask if it was hard enough, simply choose the honest answer and then he will bet you 20000 dollars to go beat his agents in the course. Beat them and then you get 20000 dollars you didnt have before.

Completing weapons training helps your rep with Mina, as does completing Stealth training with Parker.

Parker is the one who sets you up in Saudi Arabia, so get all the intel on him you can.

Omen Dang is not the assassin, so when you fight him, dont kill him and he will help you in the future.

Surkov lies to you about Brayko, so if you spare Brayko then you get a new mission you wouldnt have had, it allows you to seek out Surkov and either talk to him or kill him.

Killing innocents makes Mina dislike you, so if you want her to then kill everyone.

You can bounce between safehouses before completing missions, doing this will allow you to make contacts that will be helpful in the other countries missions. Albatross is the most valuable as he can provide you with weapons and backup during missions.

During the Brayko mission, you will have to choose between saving Albatross, downloading data, or a third option titled "Ruthless". If you choose ruthless, you will be able to accomplish both tasks and gain more experience.

Defeating bosses is easy when you build up the pistol skill and then use steel core bullets with the special pistol abilty. Once you have the ability built up you can take as much as six shots during the 30 seconds you get for the special pistol ability.

Stock up on EMPs and use them to hack all the computers so you dont have to waste time doing it the hard way. Locks to doors and safes are much easier than computers so save the emps for computers only.

Placing grenades is the equivelant to a proximity mine, they are loud but can kill up to six guys at once sometimes.

Buying intel can be expensive and sometimes not worth it. In most levels you can go to the intel section and select an option to have a snipe rifle dead dropped to your location.

Dont forget to download money in emails. I completed all but two missions the first time through with downloading any moeny in emails, then when i did it all at once i ended up with 200,000 dollars ic ouldnt spend anymore since I already had what was best.

Buying Intel to the levels isnt always helpful, but sometimes the intel actually points to more money.

When Mina asks if you have a login and password for a certain server in one of her emails, choose the snarky response that sends her a username and password, she will email you back 25000 just so you wont do it again.

Hope all this helps