Ground Zero

You've got to keep this quiet and you've got to keep whatever this is from spreading. You quietly call the most loyal and capable soldiers under your command to meet you immediately. You explain to them what needs to be done. Any still living Ashtown inhabitants must be killed, and the entire town burned to the ground. Alex must also be killed and the Shelter rendered inaccessible forever. You tell them to keep you informed at all times.

The strike team is sent in the middle of the night in Hazmat suits and tons of hardware. Everyone in Base Pandora wonders what's going on, but due to the more military mindset here, people know not to ask too many questions.

Eventually you get a message from one of your soliders.

"Uh sir, it looks like most of the town is dead already, I don't think it's airborne, because it doesn't look like the children were affected…"
"Are you sure about that? Just because they look sick doesn't mean they aren't. They could be carrying."
"Sir?"
"…I said kill everything Sergeant…"
"But I think…"
"DON'T THINK! JUST DO IT!"

The Sergeant disconnects and you can only imagine what happened next, but you don't really want to. A little while later you get another report. It's the Sergeant again, he sounds very hollow.

"Sir…it's uh over. Alex is dead…he didn't even put up a fight…we're putting the explosives in Shelter entrance as I speak…should implode and bury the Shelter from being accessible…"
"Very good. You've done a necessary thing Sergeant."
"…no I haven't…goodbye…"

You hear a gunshot on the other end followed by a bunch of other voices shouting and dead air. Your official report to the Atomic Alliance (Because it's not like you can completely cover this up) is that a ruthless gang of raiders completely destroyed Ashtown as well as the Shelter and that you're sending squads to go hunt them down.

This isn't really a satisfactory answer, but given how far away Ashtown is from the rest of the Alliance towns nobody really questions it. At least not initially.

Over the past few months you're noticeably distracted, and can't concentrate on anything. You're constantly thinking someone's going to investigate, or one of those you sent on the mission is going to blab (Now you wish they all blew their brains out) your behavior starts becoming a bit erratic as you give out strange orders to cover up things you think are going to lead to your exposure. You constantly rationalize your orders as attempting to keep the Alliance from falling, since you're convinced that everyone knew what Alex did, you'd be blamed for incompetence for allowing it to happen and without you running things you just know the Alliance wouldn't survive.

However something like this couldn't be covered up forever. Eventually someone gets suspicious of your behavior which leads to rumors, which then in turn leads to investigating. Eventually the truth comes out. The Alliance citizens are appalled, in fact if you hadn't proceeded with your extreme plan and just come out with the truth about Alex's actions in the beginning you might not have been hated quite so much.

You displayed poor judgment, by allowing Alex to go about his own devices. Strike one.

You ruthlessly had children killed to possibly contain a contagion. Strike two.

You attempted to cover all this up and lied about it. Strike three.

This type of behavior makes you look like deceitful murderous tyrant, something the Alliance towns had enough of under Harry during the Combine regime. People are calling for your blood, and your immediate resignation of Atomic Alliance leader, in fact you might be imprisoned…or worse. You've lost all support.

By the end, you've barricaded yourself in an underground room in Base Pandora with people telling you to give yourself up; of course you have no intention of doing that.

In your last moments as you point the pistol to your head, you think about Marina, and how it all would've been easier had you died with her and how you tried to rebuild civilization even after she was gone, but just failed without her around, however once again you rationalize.

"Yeah…they all united against me…I kept them united… then Vivica will certainly take power…the Alliance will live on…I didn't fail…Marina…I didn't fail…"

Your delusional thoughts come to an end with a door burst open, and a bullet to the brain.
End Of Story