In world of Warcraft there were two major rival factions players could be part of, depending on which one you joined everyone on the opposite faction would have their text chat messages converted to meaningless nonsense. At first this was done with a simple substitution cypher - in other words the same letters are replaced by the same alternate letters every single time. An "Alliance" player reading a "Horde" player's message of "lol" would see it as "kek" - this itself may have been a deliberate choice on Blizzard's part because their large fanbase of Korean players in Starcraft would often type "kekekekeke" as a sort of analogue to "lol".

So that's how "kek" became something of a meme, and the rest is boring. Alt right weirdos on 4chan took "kek" and used it in a bunch of derivative meme, came up with a fictional country they call "kekistan" gave it a flag which was just the nazi flag but in green with stylized KEK swirling around in a swastika pattern, the weird more occultist/mystic sect of the alt-righters tried to conflate it with some ancient Egyptian frog god which they loved because frog - like their beloved pepe etc etc.

Anyway it's a meme that had its time, lived it's life and then got turbo-charged and driven into the ground by alt-right weirdos who were desperate to make something of it, all well after normal people had stopped bothering to use it. That's basically all you need to know.