Very neat and chill!
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Honestly, even with a larger team 2 months wouldn't be nearly enough time to adapt the entire Epistle 3 script into a mod.
You're much better to create something small that inspired by parts of the text, or just your memories of Half-Life in general.
Hopefully it's just an outlier case and not a sign of incoming widespread abuse of itch.io's open game jam submission process, especially if there aren't moderation tools in place to counter it.
*EDIT* Well I guess there are tools after all :P
I think it would probably depend on the nature of what you make. Parody law would probably cover most people's use of the characters, but yes, anyone attempting to "actually" create a serious interpretation of Episode 3 could be breaching copyright.