setTimeout scope issue

You have to be careful with this. You need to assign your this in the outer scope to a variable. The this keyword always refers to the this of the current scope, which changes any time you wrap something in function() { ... }.

var thing = this;
thing.alive = false;
Console.log("death!");
var timer3 = setTimeout((function() {
    thing.alive = true;
    Console.log("alive!");
}),3000);

This should give you better success.

Update 2019-10-09: The original answer is true, but another option is now available for recent versions of JavaScript. Instead of using function, you can use an arrow function instead, which does not modify this:

this.alive = false;
Console.log("death!");
var timer3 = setTimeout(() => {
    this.alive = true;
    Console.log("alive!");
}), 3000);

This is supported from ES6 forward, which is part of all current browsers but IE (of course), I think. If you are using a modern framework to build your project via Babel or whatever, the framework should make sure this works as expected everywhere.