As thekaleb mentioned the creator seems to reference this symbol a lot in his games. Here is more of a back story (after some google-fu of course as I'm not very familiar with the games)

Seems like Keen 5 has it as an easter egg to reference Wolfenstein [1].

And Wolfenstein uses it since the game has a "Nazi Party" within it (if you fight them or fight with them I'm not aware of) [2].

Interesting quote from [2] "The inclusion of the swastika led to the banning of the conventional game in Germany, as cultural stigma against the swastika is high there."

[1] http://www.shikadi.net/keenwiki/Keen_5_Easter_eggs#Swastika

[2] http://wolfenstein.wikia.com/wiki/Swastika

For reference the plot of Wolfenstein is that you are a captured soldier trying to escape from a Nazi controlled castle. You are fighting against the Nazis.

While probably a mistake on John Romero's part, Keen uses 卍 in its easter egg while the nazis used 卐 instead.

True but regardless of which one is technically correct, both pretty much share the same negative connotations now. I used to always hear people talking about how the swastika is really a sign of peace, but regardless of what it originally meant, it doesn't mean that anymore.

It doesn't have anything to do with Nazis to at least a billion people in India. I'd even bet that the majority of people around the world associate swastikas with non-Nazi stuff.

It seems to be a common theme among the creators' other games, e.g. Wolfenstein 3D.