Can't get v. 1.2.1 to start

I've unzipped Knytt Stories, just to make it clear. Whenever I click on the game or the level editor, my antivirus says that a 'Virus/spyware' Mal/Agent-NL was moved to quarantine. This does not happen with the older version of 1.0.4. How do I get around this?

I'm pretty sure you're having the same problem discussed here. It all depends on your antivirus software: you could get it to ignore the stdrt.exe file (which is a false positive), but if there's no way for it do do that, I think can only disable the autoprotection system while playing KS.

Just another question. Is Mal/Agent-nl a part of Kyntt Stories? I don't want to unmark it as a virus unless I know that it is a part of it.

I think "Mal/Agent-nl" is just a label for generic malware, so no, it's probably unsafe to unmark it. If your antivirus program doesn't allow to unmark specific files, I can't think of any other options.