Windows – Microsoft Security Essentials 2.0 uninstalled themselves without me doing anything

Go in to computer management, (Click the Start Orb > Right click on Computer > Click on Manage)

Next, go down to Services and Applications > Services and look for Microsoft Antimalware Service

Make sure that this is set to Automatic.

If this is already set to Automatic, it is possible that you are simply not giving it enough time to fully start. I have seen some older machines, or even newish ones that simply have so many items set to start with the machine, it can take a good couple of minutes for the Antivirus service to start.

With Antivirus software (which Microsoft Security Essentials is), you either want it installed and running, or you want it not installed and not running. Installed but non-running antivirus software is not healthy for the computers or for the software.

Microsoft does not try to install Security Essentials. Through Windows Updates they push a small malware removal tool regularly, but you will not get a legitimate version of Microsoft Security Essentials through any method other than going to the Microsoft Security Essentials webpage and downloading it on purpose and then installing it.

Also, the time you want antivirus software (any antivirus software) running is all the time. If you have some other program you prefer and use that is installed and running, get rid of Microsoft Security Essentials. You only need one antivirus app running at a time. If, however, you do not have any other antivirus software running on your computer and you are connected to the internet or you connect removable storage devices such as thumbdrives or memory cards, you need to have antivirus software installed and running at all times.

Antivirus software is a better wall than it is a policy force. It is better at stopping infections from happening than it is at removing them once they've become entrenched. This is just a normal fact of life. Maybe needed it someday means you'll need it now so that someday is less likely to happen.

UPDATE: Ok, read up on the updates. You should not install MSE. You should uninstall it and if MS asks you to install it via update in the future, there is an option in windows update to not show that update again. This is what you should select.

MSE is not meant to be run as an on-demand scanner only. Most AV products aren't. Tools like MBAM and the others you've installer are meant, as you use them, as on-demand tools rather than real-time tools. Full AV products like MSE, Norton, McAfee, etc, are meant to be real-time tools, not on-demand only.