Alpha Protocol

First of all finish the game with rookie and then use veteran for the hard difficulty. Put all points into and master, you should master pistols for long range takes downs and quick take downs, stealth so you don't get into a huge firefight and die quickly, and shotguns for when the enemies rush(they always rush) or technical aptitude to make things easier. Invest points for the first skill of the sabotage skill to easily unlock without getting caught. Be on good terms with everyone to avoid unneeded fighting.

Then always buy intel for missions and the best weapons/armor. Always have a silencer for the pistol for sneaking. And for computer hacking you can always press start to quit the hacking without sounding the alarm. Try to not alert guards. Loading the auto save regenerates skills so you can use them again.

For boss battles use the pistols chain shot and shadow operative to take down bosses and its also useful to take down multiple enemies quickly without being seen. Brilliance also helps to finish the battles earlier.

After having just gotten this achievement I feel as though I should pass on a few things to make your trip much easier and less fraught with frustration.

INSTANT ARMOR RECHARGE - When you run out of armor (aka Endurance) hit the [ Back Button ] and then hit the [ A Button ] to enter the inventory. Exit out of the inventory and, POOF!, you have all of your armor restored. I cannot overemphasize the value of this glitch. YOU MUST STILL BE MINDFUL OF HEALTH. Remember critical hits bypass armor!

PLAY NICE – Let Shaheed live, work towards all of the romances (at least half of which give you endurance bonuses) and play nice with everyone. Anytime that you are nice to people you will probably have a much easier trek through levels at some later point.

SKILLS – Chain Shot, Brilliance and Shadow Operative are your new best friends. Using and abusing these skills will make things so much better for you. As an example of how to use these impressive skills to your advantage look at this video by SilverRagout on youtube who makes short work of Brayko on Hard:
WHAT TO TAG – I personally tagged Stealth, Pistol and Toughness. Many say not to tag toughness but I knew if I had more health I could make more mistakes. This really is your call and should be influenced by your personal play style, but this worked for me.

ADDITIONAL WEAPONS – I myself didn’t need them. Some swear by tagging two weapons (the shotgun seems pretty popular for close takedowns) but I only used my shotgun once and didn’t waste any points on it. Instead I would focus on, and I know this sounds ludicrous, melee combat. I found it easier to punch and kick my way free of kamikaze attackers than trying to switch out my weapons. As an added bonus you also get some reduced damage from melee attacks as well. I would NOT tag melee but I would spend any additional points on it you could.

VETERAN – As others rightly say, complete the game on Recruit first. Then use the Veteran background for your hard play through. It makes it as though you were starting on level 9 or so. It certainly helps a lot.

MISSION ORDER – Do Rome, Tai Pei and then Moscow. In that exact order. And do all missions available in any region before the red-highlighted alpha missions. These tend to involve boss fights and you need to get as much experience and levels before attempting them as you can. This doesn't mean you can't skip around just that you should do all missions before the red-colored ones that you can.

EMP & HEALTH – Be sure to get at least the first skill in Sabotage. This allows you to use an EMP to open doors and disable computers instead of doing it manually! An absolute MUST! Especially later in the game! USE BOTH AS OFTEN AS YOU CAN. Especially since by using them you get perks that allow for even more effective use. After using the EMP 25 times you get Electronic Warfare, which gives you an additional EMP per inventory slot. After healing 2000 points you get Self Made Medic, which allows you to carry an additional First Aid Kit per inventory slot AND makes all healing 10% more effective! Work for these early!

WHAT TO BUY – Only buy Intel that gives tangible benefits in a mission, do not waste money on Dossier information at all. Buy Health Kits and EMPs as well as the upgrades for both types of items. The Advanced Stealth Armor (for the main game) and the Advanced Combat Armor (for the last mission) are both very good. You use the combat armor for the last mission because you will not be sneaking at all and it gives +20 on Endurance/Armor over the stealth version.

!! SPOILER !!
MISSION SPECIFIC

MADISON OR THE BOMB? – Always save Madison. As you approach where she is being held you can take out several guys from above and can easily dispatch the two or three that appear later when you see her. Then take out the guy in the elevator.

JIZAN STOCKPILE – You may want to skip this mission entirely as the end was brutal for me on Hard.

END GAME – With Sie as your handler for the last mission, try to convert Parker on your side in the end. This way all you have to do is protect him through the endurance fight. Sie is a one woman killing machine and helps out a ton here, so you can simply stay back and help her pick off the hordes of bad guys.

DARCY – When dealing with Darcy during the last mission stay where you are when the fight starts and pick off as many people as possible, then make your move to the tower. You should know that the bad guys will continue to respawn so do not get too caught up in this activity.

GET TO DA CHOPPAH – Kill the bad guys while you are somewhere the helicopter cannot shoot you. (Duh!) A good place to do this is where the second missile launcher is located. Then you can focus all of your attention on the chopper. Always run! (Hold A)

Not a full on solution, but a method I used to great effect throughout the entire game.

With Chain shot, pressing B cancels out of it, without using up any of the cooldown. This means you can activate Chain shot, spend ages lining up the shot, press B then shoot them. It has to be a very quick transition from B to RT else the target will have moved too much to be effective.

Using this sequence I defeated Deng with out being touched, having to run around, lay grenades, anything as everytime I shot, I instantly hit LB to bring up chain shot again. Just be carefull not to it RT before B, else you will be unable to cancel out.