Alpha Protocol Wiki

Beneficial Mission Order is a walkthrough focused on showing how various missions interact with each other, depedning on the order they are completed.

Main article: Missions.


Alpha Protocol is a mission-driven game where the player may control (to some extent) the order in which they do these missions. The chosen order will have all kind of effects on both the story and the XP/money/perks received, and also the equipment available at the Clearinghouse (the store, for short). Here we will try to list all the possible effects for each mission.

We will not discuss the consequences impacting the story and characters in too much detail — see the lore pages for that. General consequences that depend on how a mission is done are also out of the scope of this page, unless when is also a factor. For seeing the "how" parts, we recommend visiting the individual mission pages and checking out the "Choices and Consequences" section at end.

Saudi Arabia[]

Here is the recommended mission order for Operation Desert Spear:

Intercept Nasri the Arms Dealer[]

Purchase all the equipment you'll need later, before doing this mission if you're planning to kill Nasri, as that greatly reduces the store selection.

After this mission is completed the following intel disappears from the store (but remains in effect if already purchased): Additional On-Site Acquisition #1 ($3,000) — Additional supplies added to the Investigate Weapon Stockpile mission area.

  • Extorting Nasri replaces the above intel with the another one that costs $4 instead. Store selection is unaffected.
    • Additional On-Site Acquisition #2 ($4) — Additional supplies added to the Investigate Weapon Stockpile mission area.
  • Arresting Nasri nets you a +1 reputation with Mina if Bug Al-Samad Airfield is done after. Store selection is only slightly reduced. Also makes the following intel appear:
    • Mission Intel ($3,500) — Bonus Objective added to Investigate Weapon Stockpile mission.
    • Supplies intel option appears for the Investigate Ruins Transmission mission in Rome.
  • Killing Nasri nets you a -1 reputation with Mina if Bug Al-Samad Airfield is done after. Store selection is greatly reduced (leaving ammo/basic gear only).

Bug Al-Samad Airfield[]

  • Receiving Sean Darcy's dossier information from Mina during this mission's briefing allows you to get Darcy's secret fact during Investigate Jizan Weapon Stockpile mission's briefing.
  • Defeating Shaheed's elite guard reduces the difficulty level of certain enemies in the following two missions.

Investigate Jizan Weapon Stockpile[]

Benefits from being done last out of three, as you would be able to reach Level 4 and unlock additional abilities. This helps with a relatively difficult battle at the end of the mission. For a stealthy playstyle, this gives access to Shadow Operative and enables to achieve 100% enemies evaded.

Intercept Shaheed and Recover Missiles[]

Free Roam[]

The "free roam" portion is the largest part of the game with a lot of missions and choices. You can visit any of the 3 hubs in any order, and abandon the operations at any point to go do missions in other hubs (except for the very last mission in Moscow).

If you wish, you can commit to a single operation and not leave the location until it's fully done. However, the optimal order requires you to jump between hubs to do the conversation-only and easy missions in all 3 operations first, and only then focus on combat-heavy missions with lots of enemies.

Although, the difference between optimal and normal order is not very significant, and mostly becomes relevant when playing on Hard difficulty as Recruit, or when doing challenge runs, where you actually need to plan the character build in the early game. When playing as Veteran with no restrictions, missions can be done in any order without much hassle.

We provide the unsorted mission list first and then the recommended order after.


Contact Grigori the Informant[]

  • Grigori is a major source of intel for Moscow and other hubs, who offers several exclusive dossiers. Always visit him first, if you care about intel.
  • Provides access to Tech-focused equipment and Advanced Utility Armor.
  • The way you interact with Grigori will ultimately influence all the missions involving Sergei Surkov.
    • Antagonizing Grigori with violence or aggressive dialogue options will prevent you from turning Surkov into an ally, but would still allow you to ally with Konstantin Brayko in the end, if you let him live and don't arrest him in Assault Brayko's Mansion.
    • Being on good terms with Grigori via suave and professional dialogue options will unlock a bonus objective in Assault Lazo's Yacht, and enable you to turn Surkov into an ally. This is the recommended option.

Assault Lazo's Yacht and Retrieve Data[]

  • Being on good terms with Grigori unlocks an optional objective Hack Lazo's Computer worth $10,000 + Russian Mafia dossier.
  • Spare Sis to unlock the Contact Albatross mission.

Contact Albatross[]

Investigate Weapon Shipments[]

Intercept Surkov at US Embassy[]

Contact Surkov at Moscow Office[]

  • No matter what you say here, Surkov agrees to help you.

Assault Brayko's Mansion[]

  • Meeting with Steven Heck before this mission and having a positive reputation with him after Taipei, will allow you to buy intel to spike Konstantin Brayko's cocaine, making the fight against him much easier.
  • Depending on your choice the handler (either Albatross or SIE), they may die by your hand. This make his/her help unavailable in later missions.
  • Going after Halbech data unlocks the Prevent Surkov's Escape mission, if the right dialogue options with Brayko are also chosen. Saving ally provides a perk and XP. Doing both requires being a Veteran or Tech Specialist, or having 8 ranks in Technical Aptitude.
  • Konstantin Brayko will become your ally if you accept his bribe of $70,000 and let him go, and ask him to execute Surkov in Prevent Surkov's Escape afterwards.
  • Being allied with Brayko allows you to buy additional intel for Investigate Delivery at Warehouse that turns the Mafia members friendly.

Prevent Surkov's Escape[]

  • This mission disappears if you leave Moscow and not do it immediately.
  • Depending on your choices here, you may become allies with Surkov or Brayko.
  • Either accept Surkov's deal right away, if he's friendly, or decline and then chase after him for extra dossiers and money (which always happens if he was hostile at the Embassy). If Surkov was friendly initially, then not executing him on the helipad would still allow you to keep him as an ally.
  • Brayko becomes your ally if you accepted his bribe of $70,000 and let him go in the Mansion, and ask him to execute Surkov when given the option here.
  • Becoming allies with either allows you to buy intel from their Russian associates and turn Russian Mafia members in Investigate Delivery at Warehouse friendly.


Contact Steven Heck[]

Contact Hong Shi[]

  • Meeting with Hong Shi unlocks the Rising Sub supplier of equipment and intel. They provide 3-stars SMGs, some good high-end armor mods and gadget upgrades.

Assault Triad Headquarters in Slums[]

  • Not blackmailing Hong Shi and keeping the reputation with Hong Shi positive will enable the Triad's help during Stop Omen Deng at Memorial Rally and allow continued access to the Rising Sub supplier.
  • You lose Hong Shi's support and his supplier if you blackmail him or end up with a reputation of -1 or lower after this mission.

Investigate Warehouse District Data Trail[]

  • If you've had G22's support before this mission you may lose it here by refusing to delete the bugs at the end.
  • You can keep G22's support and the dossier intel with no penalties, if you Bluff Albatross in the end after bugging all 6 servers.

Retrieve NSB Data from Grand Hotel[]

  • If you blackmailed or have negative reputation with Hong Shi, you will lose access to Guard Reassignments intel for this mission.
  • This mission offers a lot of opportunities to gain or lose reputation with Steven Heck and Scarlet Lake, which can affect them in the future: Heck can possibly betray you at -1 at the end of Taipei operation, and Scarlet's romance unlocks at +6.

Intercept Assassination Plans[]

  • Added Handler Support intel: G22 agent is a possible handler for this mission if you're allied with Albatross.
  • The choice between saving the data on Riots or Assassination at the end determines how the final two Taipei missions will play out.

Contact President Sung[]

Stop Omen Deng at Memorial Rally[]


Missions Identify Jibril Al-Bara at Chateau, Bug CIA Listening Post and Intercept NSA Intelligence can be done in any order and mostly affect Mina Tang's, Marburg's, and Leland's reputation, and news reports. Avoid killings anyone during these missions to earn +2 reputation with Conrad Marburg.

Identify Jibril Al-Bara at Chateau[]

  • For identifying all guests you earn a useful perk: On the Guestlist — 5% Intel Discount from all sources.

Bug CIA Listening Post[]

  • There is a possibility to acquire an ultra-expensive armor mod during this mission, long before it becomes unlocked in the store. The mod is inside the armory on the 3rd floor and chosen randomly out of 4 options: Improved Digital Camouflage (very good for stealth), Advanced Ceramic Plates (best combat mod), Adrenaline Optimizer (good general mod), or Carbide Matrix (decent combat mod). The desired mod can be save-scummed for. There is also a guaranteed Silencer Mk3 mod in the armory.

Intercept NSA Intelligence[]

Contact Jibril Al-Bara/Halbech Informant[]

  • Conrad Marburg's reputation can be swayed to either side in the conversation here (from -7 to +10), which will influence the interactions him during Intercept Marburg at the Museum of Art.
  • Having a reputation with SIE of 0 and higher decreases your reputation with Marburg (-1).
  • Having a reputation with SIE of -1 and lower increases your reputation with Marburg (+1).
  • Ending this mission with negative reputation (-4 or lower) can enable you to kill him in Intercept Marburg at the Museum of Art.

Investigate Marburg's Villa[]

Investigate Delivery at Warehouse[]

  • Being allies with Surkov allows you to buy intel from his Russian associates and turn Russian Mafia members to your side in this mission.
  • Same exact intel is available if you are on good terms with Brayko: i.e. you accepted his bribe of $70,000 and let him go, and afterwards asked him to execute Surkov in Prevent Surkov's Escape.

Investigate Ruins Transmission[]

  • After both "Investigate" missions are completed you'll get a scene where you can choose to romance Madison, if her reputation is at +3 or higher.
  • Romanced, or not, if you get Madison's reputation to +3, you unlock her secret fact, which allows you to goad Alan Parker into attacking Marburg, letting you kill him afterwards in the endgame mission.
  • There are no benefits to having negative or neutral reputation with Madison.

Intercept Marburg at the Museum of Art[]

  • Right before this mission a supplier called The Turk should unlock, who provides a lot of high-end equipment (most notably 3-stars shotguns and Advanced Stealth Armor).
  • Having high reputation with SIE makes the following intel available: Bomb Timer Delays ($2,600): +1 minute for the bomb defusal timer (useless).
  • (?) Dealing with Marburg here, without meeting SIE first, may increase your reputation with her when you do finally meet her in Investigate Weapon Shipments.
  • Conrad Marburg can be fought to the death in Rome, if you Taunt him twice when speaking to him after he interrupts the battle. The requirements are:
    • Negative reputation with Marburg (-4 or lower), which can only be achieved in Contact Jibril Al-Bara/Halbech Informant.
    • Suave is your most often chosen dialogue stance throughout the whole playthrough.
    Otherwise, he escapes, but can be fought later in the final mission, or made neutral, with correct choices.


Infiltrate Alpha Protocol[]

Recommended Order[]

By following this mission order you will get the benefits of: maximized intel and store selection, lots of easy XP to level up, free equipment and perks that can save you money, and additional dialogue options.

Your actions in Rome do not not affect Taipei, and Taipei does not seem to affect Rome either. So you may safely jump from Taipei to Rome, or from Rome to Taipei whenever you wish. Both of them affect Moscow and Moscow affects them both, so it works best if the first few missions from Moscow are done in the middle, and then Moscow only fully finished last. Note that when it comes to more difficult missions (Intercept Surkov at US Embassy, Intercept Marburg at the Museum of Art and Investigate Warehouse District Data Trail) you can always leave them for later and come back when ready.

The first part is mostly "introducing yourself to people and getting free stuff" (1-4), with very few consequences for later missions, as long as you stay diplomatic and avoid killing major characters or civilians. The second part (5-7) is where most of the game's events happens and where the choices you make actually matter.

0. Graybox[]

  • The one thing you should decide from the start is how you would prefer to handle Marburg:
    1. Kill Marburg in Rome: choose Suave options more often than others over the whole playthrough, get Marburg's reputation low (-4) when you meet him.
    2. Get Marburg to kill Parker and fight him in the endgame: unlock 83% of Marburg's and 80% of Parker's dossier (need 2 Parker's dossiers from Graybox + 2 Mina's e-mails in the mid-game). Can also be done via the secret fact from Madison.
    3. Turn Marburg neutral in the endgame: unlock 83% of Marburg's dossier, but avoid unlocking Parker's dossier past 60%.
    4. Or do none of the above and select any of the normal dialogue options with Marburg to never see him again after the initial conversation in Infiltrate Alpha Protocol.

1. Moscow[]

  1. Contact Grigori the Informant: for a lot of unique intel and Tech equipment. Should be visited first before Rome and Taipei if you want extra dialogue and 100% of the dossiers. Be Suave with him for best results.

2. Rome[]

  1. Identify Jibril Al-Bara at Chateau: a lot of easy XP. Perk: 5% Intel Discount from all sources — will affect all following missions.
  2. Bug CIA Listening Post: grab a free high-end armor mod for your chosen playstyle + Silencer Mk3 from the armory.
  3. Intercept NSA Intelligence: finish this, but don't contact Marburg after if you want to see his reaction to SIE.

3. Taipei[]

  1. Contact Steven Heck: for intel and gadget equipment, plus help with Brayko.
  2. Contact Hong Shi: for SMGs, armor mods and gadget upgrades.
  3. Investigate Warehouse District Data Trail: if you're good with stealth, you can do it right away, if not — leave for later. Bluff Albatross at the end for the best results. Can be done after Contact Albatross later for a slightly different dialogue (and the same outcome).

4. Moscow[]

  1. Assault Lazo's Yacht and Retrieve Data: spare Sis to ally with Albatross.
  2. Contact Albatross: for intel and Stealth-focused equipment.
  3. Investigate Weapon Shipments: to unlock SIE for other missions and get $50k from Grigori.
  4. ~ Intercept Surkov at US Embassy: do it here or leave it for later, after Rome and Taipei.
    • the choice of the handler here decides the future ally for the Mansion, so you may want to leave it for later if you want to experiment with different handlers during the Mansion mission without having to redo a lot of prior missions.
    • unlocks SIE (only if she's the handler) and Surkov (if he's friendly) as store suppliers of Combat-focused equipment — if you're going for a run-and-gun build it's worth to try and rush this mission for the 3-star weapons and Advanced Combat Armor;
    • if you're going for a stealth build, then there are no benefits to doing this early; in fact, you probably won't have the required abilities (high level Shadow Operative, Remote Hack, Binary Invisibility) to do it without detection at this point.

5. Taipei[]

  1. Assault Triad Headquarters in Slums: decide if you want the Triad's help in the last Taipei mission (they're bad for stealth characters there, because they trigger alarms); if not, blackmail Hong Shi for money/intel but lose his store supplier.
  2. Retrieve NSB Data from Grand Hotel: lots of opportunities to lose or gain reputation with Heck and Scarlet.
  3. Intercept Assassination Plans: decide here if you want to prevent Riots or Assassination.
  4. Contact President Sung
  5. Stop Omen Deng at Memorial Rally: fight Omen Deng (the easiest of Brayko and Marburg). Spare him for more possibilities during the endgame. Listen to Sung's speech for another Perk: 5% Intel Discount from all sources. Heck can betray you at end if you get his reputation too low (-1), but will never do it if you haven't finished Brayko's Mansion yet.

6. Rome[]

  1. Contact Jibril Al-Bara/Halbech Informant: decide if you want to either kill Marburg in Rome (then lower his reputation with Suave choices and be sure you were Suave most of the time throughout the game) — or to keep him neutral (then his reputation doesn't matter, as long as you unlock at least 83% of his dossier while in Rome).
  2. Investigate Marburg's Villa: choose SIE if you want some funny commentary (no real benefits other than that). Choosing Madison can help increase her reputation, but it's not required for her romance (+3 reputation) if you've made correct choices with her earlier.
  3. Investigate Delivery at Warehouse: if you do this before finishing Moscow and allying with either Surkov or Brayko you will lose the intel that makes the Mafia friendly (irrelevant, as it barely changes the mission).
  4. Investigate Ruins Transmission: after both "Investigate" missions you can romance Madison (or not) and unlock her secret fact.
  5. Intercept Marburg at the Museum of Art: kill Marburg here if you've got his reputation down to -4 and was Suave for most of the playthrough. Or leave him for the endgame for more possibilities.

7. Moscow[]

  1. ~ Intercept Surkov at US Embassy: if you didn't do it before, finish it here.
  2. Contact Surkov at Moscow Office: none of the choices matter here, as Surkov's attitude is determined by the first meeting with Grigori.
  3. Assault Brayko's Mansion:
    • Brayko is the hardest boss in the game, so it make sense to leave him for later.
    • if you have the right class (Veteran/Tech Specialist) or the right skill (Technical Aptitude at 8), the option to save both Halbech data and the ally will be available.
    • if it not, choose data over ally, as they can escape themselves.
    • interrogate Brayko with correct choices (see the mission's page) to unlock the final mission.
  4. Prevent Surkov's Escape: either accept Surkov's deal right away, if he's friendly, or choose to chase after him for extra intel and money (which always happens if he was hostile at the Embassy). Or become allies with Brayko by letting him execute Surkov. The choice will only affect some ending dialogue.