Safehouse Trophies are items of note from memorable moments. Across his many operations, Michael Thorton will come across several individuals with inevitably noticeable items in his encounters with the various people he meets. Aside from special, customized Trophy Weapons of varying types looted from fallen enemies for personal use or sale, Michael will also take souvenirs that happen to catch his eye in spur of the moment occurrences throughout his missions. Some items of interest will also be sent to Michael by people he knows or meets. These items are representations of memorable moments, each sparking a recollection or reflection by Michael himself upon examination.
Safehouse Trophies are on display in various places in each Alpha Protocol safehouse used by Michael Thorton throughout his operations. Examining each item using the sprint button/key will result in Thorton recalling the person or the conditions from which he had received that exact item aloud.
| Trophy | Acquired From | Examination Commentary |
| Heck's Detergent Bottle | Positive reputation with Steven Heck | It's signed "Good times - Steven Heck" . Yeah... |
| Heck's Cigar Clippers | Negative reputation with Steven Heck | I have a feeling Heck isn't a big fan of me right now. |
| Darcy's Photo | Positive reputation with Sean Darcy | Oh great. A picture of Darcy. He wrote "Mike and Sean, fuck yeah!!!" ...With three exclaimation marks. |
| Madison's Headband | Seduce Madison Saint James | (If alive) Madison... Good times... I wonder if she's ever gonna call... (If dead) Sorry Madison... |
| Trophy | Acquired From | Examination Commentary |
| Brayko's Knife | Defeat Konstantin Brayko (Executed or Spared) | I think there's enough coke residue on this knife to get very, very high. |
| Brayko's Jacket | Kill Konstantin Brayko | How many gay cheetahs gave their lives for this jacket? |
| SIE's Kneepad | Attack and defeat SIE at the end of Investigate Weapon Shipments | Why do I get the feeling that she actually likes that I shot her repeatedly? |
| Sis' locket | Kill Sis | It's Sis' locket... It's got an image of St. George. Guess it didn't protect her from me. |
| Marburg's Pen and Gloves | Kill Conrad Marburg in Rome | Sorry Marburg, mess with an Alpha Protocol agent, you get burned. |
| Nasri's beret | Kill or arrest Nasri | (If killed) Hm, Nasri. Why can't all terrorists be as fun to kill as you? (If arrested) I sure hope Nasri likes waterboarding... |
| Glass Eye | Kill Al-Samad Lieutenant in Intercept Shaheed and Recover Missiles | I probably didn't need to take his glass eye as a trophy, but... ears are so passé. |
| Trophy | Acquired From | Examination Commentary |
|
Brayko's Sound System |
Spare Brayko and accept his bribes (Only appears in Moscow Safehouse) |
No comments from Michael, but it turns on disco lighting and plays “Turn Up The Radio” by Autograph, the song that played when fighting Konstantin Brayko. |
| Hong Shi's Ceremonial Sword | Complete Contact Hong Shi | I appreciate the gesture, but... Hong Shi could have gotten me a real sword... |
| Shooting Range Plaque | Complete shooting range with a score of 100 or greater | (Negative reputation) Mina gave me this for aceing the shooting range. I guess that was nice of her. (Positive reputation) Mina wrote 'Way to score'. I think she custom framed it just for me... How nice. |
| Stealth Course Plaque | Complete stealth course with a score of 100 or greater | There's a note from Parker here... 'The agency made me give this to you.' What a guy. |
| Gadget Course Plaque | Complete gadget course with a score of 100 or greater (Lost upon gaining negative reputation with Sean Darcy) | Agent Darcy sent me this for acing the training course. He misspelt my name 'Thornton'. |
| Darcy's Photo | No requirements | Hey look... Darcy photoshopped our faces into a still frame of a buddy cop movie. That's um... yeah. |