In a cutscene of "McKenzie Airbase Interior" from 2, one particular U.S. airforce soldier helps Lian escape by unlocking a window without sounding the alarm, as he has "took an oath to uphold the law". Based on the Enlistment Oath, all members of the U.S. armed forces must “preserve, protect, and defend the Constitution of the United States against all enemies, foreign and domestic.” Hence, the pledge clearly states that all soldiers must abide by constitutional laws and regulations. Soldiers can refuse a direct order if the said order is unlawful or if it violates the Uniform Code of Military Justice. With that being said, the airforce soldier has his reasons to help Lian, as the Agency operatives are impersonating FEMA and actively trying to have Lian killed, both of which do not follow the protocols. Also, even if Lian is really a wanted criminal, she deserves a fair trial instead of an assassination in a hospital as it is her civil right.
The primary goal of "Hotel Fukushima" level from 3 is to eliminate Shi Hao and his fellow rogues. The player has a choice to make Gabe save the captured JRA member by killing Shi Hao and the grunts accompanying him in the same room so the JRA member can flee, or Gabe can let Shi Hao or his grunts kill him. Additionally, Gabe can kill the JRA member himself after killing Shi Hao. Letting the JRA member die or killing him doesn't have penalty while helping the JRA member will result in him thanking Gabe for saving his life and giving Gabe MIL-15, an extremely deadly weapon, before running away after Gabe threatens to kill him and tells him to get lost. Gabe's O.O.C. Is Serious Business is extremelly fitting considering JRA is a rebel group infamous for carrying many international terrorist attacks and saving their low rank member won't benefit Gabe at all except for short-term power in the form of MIL-15.
Jason Chance is killed by being knocked back into the tail rotors of a helicopter with an UAS-12 while wearing full bulletproof body armor, yet, when Gabe Logan is shot by an UAS-12 during normal gameplay, he manages to stand completely still despite only wearing a basic flak jacket. How does he do that?
Why would killing Foreman Jones in Syphon Filter 3 after interrogating him result in a truck suddenly trying to ram Mujari? Was it some kind of automatic countermeasure set by Jones just in case he was killed, or did someone drive the truck? The game made no explanation about this.
In "Docks Final Assault", if Gabe Logan either kills or ditches Nigel before finding the last containment truck, Nigel will say "Curse you, Logan!" as his final words. Why did Nigel say something like that? Nigel is a double agent, so by norm he should've expected some betrayals since he makes a living by deceiving and betraying people.
It is weird and almost funny how Jonathan Phagan's attempts of bribing everyone he meets always end in failure. We can understand how a stoic agent like Gabe and a nutcase like Mara cannot be bribed into not killing or capturing him, but why would it not work with anyone else?
One cutscene of "Agency Bio-Lab" level in 2 shows Ramirez asking an agency operative for help because he is feeling sick. Many fans in the past joked about him getting a flu because he spent hours (if not days) in Rocky Mountains during a cold temperature while wearing a tee shirt. But the horror realization comes from the agency operative's harsh reply, telling Ramirez to shut up that soon he won't have to worry about anything. It is possible that Ramirez is also infected with Syphon Filter virus, and Gabe does not know about it.
Also in "Agency Bio-Lab", when Gabe retrieved his gear from the locker, it is revealed that he didn't have non lethal weapons such as stun gun on crossbow with transquilizer arrows like he had when he revisited Pharcom Expo Center to get the data disc encryption codes and to take down Morgan. At that time Gabe didn't believe in mercy and was certain that everyone working in the lab deserved to die, whether they were agency opeatives or researchers. The only reason Dr. Elsa Weissinger survived (at least until Dark Mirror bonus level) was because Gabe needed her to synthesize the vaccine for Lian and she ran away while triggering the alarm before Gabe could kill her.
When Gabe is escorting Phagan to Lian's cell in Stronghold Catacomb from the first game, both are ambushed by many of Rhoemer's mooks who immediately open fire. Phagan, instead of saying something like "Watch out!" or "Please protect me!" like you expect from a wimp like him, he tells Gabe to " Kill them!" nonchalantly. Sure, Rhoemer's mooks are determined to not let either Gabe or Phagan leaving the abandoned cathedral alive, but Phagan wanting Gabe to kill them is a glaring sign that he is probably used to seeing people dead around him. It also serves as a nice reminder that Phagan is not an ordinary helpless old man, but a death merchant who earns profit in unethical ways with his Pharcom medical company as a front.
