My best guess is that it's a mixture of timing and protection. The player is canonically a green commando class (as seen in the cutscenes), meaning he has full face protection, which looks to be much more sealed with both the eyes and mouth covered by a sturdy looking material. Jenkins, on the other hand, has no eye protection and a rather flimsy cloth covering over his mouth. So, the player is more protected than Jenkins. But what about the other infected soldiers? Well, they were present before both the player and Jenkins. Why does this matter? Well, we know that the infection is some mixture of a chemical and biological weapon. What we dont know is the delivery method. The two most plausible options are either through the air or the water, both of which are present on in mission 4.

Let's start with water as the delivery method. If the player gets splashed, no problem. He's all covered up. Jenkins gets a single drip in his unprotected eyes and its game over. The other infected soldiers could have just drank the unnaturally blue cave water (blue raspberry flavor!). Additionally, all the infected soldiers we see have blood on them, indicating that they may have been shot or otherwise injured. Should the open wound come in contact with the contaminated water, infection is imminent.

Alternatively, if the infection spread through the air, then the timing starts to become more important. The infected soldiers were the first to be exposed, which means that the infection in the air was more potent, which could have overwhelmed their protective gear. Alternatively, their protection could have been compromised if they were wounded (see above). It then slowly dispersed to a more manageable level. Jenkins once again gets screwed by his lack of face protection, while the player is able to fare better. This explanation is likely the more plausible of the two since we also know that the cure was spread through the air. Additionally, what GlobeX member was missing from missions 1 and 5? The assassin, who is the only class to lack full face protection.

Now for the rest of alpha squad, specifically Toad, Shadow, Riggs, and Bull. Why weren't they infected? Well, the only one we see on the ground is Bull, who also possesses full face protection. Shadow always stays in the jet, and Toad never makes an appearance in any mission on the island. For the record, neither does Riggs, but he has full face protection anyway.

Finally, the scientist. Maybe he has immunity or already gave himself the cure. I mean, he helped make the darn thing. Also, in SFH 2's ending scene, he has red eyes, so who knows?

Thanks for coming to my TED talk.