PLOT RELATED TROPHIES:
Desert Spear 
Assassinate Sheikh Shaheed.
This trophy will either be awarded at the end of the mission "Intercept Shaheed and Recover Missiles" or at the end of the "Contact Sheikh Ali Shaheed" mission you do just before infiltrating Alpha Protocol. In either case, using the "Execute" command will terminate Shaheed and earn you the trophy.
Stay of Execution
Allow Shaheed to Live.
This trophy will be awarded at the end of the mission "Intercept Shaheed and Recover Missiles" if you choose the Professional stance and spared his life.
Secret Service
Prevent the assassination of President Ronald Sung.
This trophy will be awarded at the end of the mission "Stop Omen Deng at Memorial Rally" if you choose to save the Assassination data from the flash drive gained at the end of the mission "Intercept Assassination Plans".
Keeping the Peace
Prevent a riot from killing hundreds in Taipei.
This trophy will be awarded at the end of the mission "Stop Omen Deng at Memorial Rally" if you choose to save the Riot data from the flash drive gained at the end of the mission "Intercept Assassination Plans".
A Plot Uncovered
Discover the identity of Sung's assassin.
Depending on your reputation with this character, this trophy will be earned in one of three places.
Spoiler! (click here to reveal)
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- If you spared Deng at the end of the "Stop Omen Deng at Memorial Rally" mission, you can receive a message from him during the "Infiltrate Alpha Protocol" mission that contains the answer. When using the computer to contact Parker, you will also have the option "Download to PDA" which will trigger his message, informing you that Scarlet was captured on film with a sniper rifle at Sung's assassination.
- If you have a high enough reputation with Scarlet, she will confess to being the assassin during the "Infiltrate Alpha Protocol" mission if you encounter her in the interrogation room. She will only be there if you had previously visited her in the "Contact Scarlet Lake" mission prior to starting "Infiltrate Alpha Protocol"
- If you skip visiting Scarlet in the "Contact Scarlet Lake" mission, during "Infiltrate Alpha Protocol" she will not be in the interrogation room. At the end if you face Leland and spare his life, she will appear and shoot you in the back. When you realize that the assassin was Scarlet, the trophy will pop.
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Never Trust a Sociopath
Alienate "secret agent" Steven Heck.
Spoiler! (click here to reveal)
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Steven Heck is a little nuts, but if you piss him off, he's downright scary. When you start to complete missions in Taipei, do all other available missions before going to contact Steve.In your first meeting choose Professional four times, then Aggressive for the fifth and sixth response.In Grand Hotel Mission briefing use Professional choices, warn against killing civillians and do not destroy Heck's file. When you receive his mail, don't respond to it right away, but hang on to it for emergencies. You should still be able to get down to -10 before starting the "Intercept Assassination Plans" mission, which is good because you'll win a point back just for including him in the carnage. After the mission is over you can respond to the email in order to bring you back down to -10.
You won't get the trophy until you have completed "Stop Omen Deng at Memorial Rally" during the news report. Heck will contact you and you and if he still hates you enough, he will tell you that he gave your name to the cops. The trophy will pop just in time to hear the newscasters call you out by name.
NOTE: Heck will not turn you in if he is the only available handler for the "Infiltrate Alpha Protocol" mission. So ensure that you have not alienated/killed both SIE and Albatross, so that one of them will be available to replace Heck. If you complete all of the Taipei missions first, Heck will not turn on you to prevent the possibility of having no viable handlers for the final mission.
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Hard Choices
Stop the plot to destroy the Roman History Museum.
In the mission "Intercept Marburg at Museum of Art", choose to enter the East Wing. The trophy will be awarded at the end of the mission.
Friends Before Strangers
Save Madison Saint-James from certain death.
In the mission "Intercept Marburg at Museum of Art", choose to enter the West Wing. The trophy will be awarded at the end of the mission.
Respected Enemies 
Gain Marburg's respect and best him in combat.
See
Youth Trumps Experience.
Youth Trumps Experience
Provoke Marburg into a fatal duel.
Spoiler! (click here to reveal)
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For these two trophies, your reputation score with Marburg is key. Obviously for Respected Enemies you will want a high reputation, and for Youth Trumps Experience a very low reputation.
Important Note: Marburg's reaction to you is affected by your overall choices throughout the entire game up to the point you encounter him. If your total number of Suave choices exceed the total Aggressive or Professional choices, you will receive -1 reputation with Marburg. If your total Aggressive is higher, there will be no change, and if your total Professional choices is higher you will receive +1 reputation. This is checked once during the "Contact Jibril Al-Bara" mission, and and once at the start of your fight with him in the museum for a possible range of +2 to -2.
What may also be a factor is completing your dossier on Marburg, as that will sometimes have an affect on what options are available in the dialogue. You can get it to 100% before the fight, which will net you the "Know Your Rival" perk and give you an extra 5% damage.
Marburg Dossier locations:
- First arrival at Rome safehouse (16%)
- CIA Listening Post - 2nd Floor, north east room against north wall near whiteboard. (33%)
- Email from NSA Echelon tap (50%)
- Purchased mission intel for "Contact Halbech Informant" (66%)
- Secret room behind garden hose in Marburg's Villa (83%)
- Door just to left of East Wing entrance in Museum (100%)
During the Cafe talk, the following other factors will also have an affect on Marburg:
- SIE (if alive): Positive rep (-1 Marburg) / Negative rep (+1 Marburg)
- No enemies alerted/killed in either the "Bug CIA Listening Post" or "Intercept NSA Intelligence" missions, and did not kill Al-Bara (+2 Marburg)
Conversation Path for Maximum Reputation Loss:
- Cafe conversation
- - - - - - - 
- Villa conversation
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- Bomb defuse conversation
- - - 
- Mid-battle conversation
- 
Conversation Path for Maximum Reputation Gain:
- Always pick

By the end of the boss fight in the Museum if your reputation is at +6 or higher with Marburg, you will have the option to let him go, netting you the Respected Enemies trophy. If he is at -6 or lower you will provoke him into finishing the fight instead of fleeing, unlocking Youth Trumps Experience after he is dead.
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One Less Gangster
Eliminate Konstantin Brayko.
See
A Price on Mercy for Boss strategy on Brayko.
A Price on Mercy
Spare Konstantin Brayko.
At the end of the mission "Assault Brayko's Mansion" you will fight, shockingly enough, Brayko. This is a tricky fight, but using a combination of the Chain Shot skill and running like a frightened girl you should have no trouble defeating him. When he snorts coke and hulks out he will run at you and unleash a devastating knife slash attack that hits multiple times and staggers you slightly. Sprint away and lead Brayko onto the stage, then jump off the edge. Repeat this until he loses his buzz and falls to his knees swearing. Line up and take a few more cheap shots at him, preferably with Chain Shot if it has recharged. Usually about two or three uses of the Chain Shot skill will bring him down. If you have met with Steven Heck prior to the mission, you can also buy an intel option to have Brayko's drugs poisoned to take some of the fight out of him. Once he has been defeated, choose to "Execute" him for the
One Less Gangster trophy, or choose to spare him for the
A Price on Mercy trophy.