This was... straight up annoying to read. At first, you dump ridiculous amounts of backstory on the player, full of weird concepts and names they have to remember... and then you introduce the alien rules, who speaks in a manner that was SO ANNOYING that I genuinely just shut off the game on the spot. Did you think it was funny? Because it was not. I genuinely had to play it again to finish it.
Also, all of that backstory? Pointless and not relevant to the story, since the actual story is about fighting pirates. Why wasn't I simply hired? I genuinely don't really care about the Crypt Shyfter metaplot, and I doubt many people will. I don't care about continuity, I care about THIS story being fun. Continuity is a bonus and should never take precedence.
Tips: don't smack player/reader in the face with a ton of backstory and new names, introduce them gradually.
And don't make characters speak in weird manner, including phonetic accents or other quirks - it's always annoying to read.
Also, it's a bad form to introduce a character that has a previous relationship with the player character, and e.g. have the PC *love* that character. Like, why? *I* don't love that dude, and I am my character. I should be able to decide what I feel, obviously! Don't tell players what they feel, or what their characters feel if you're not 100% sure that player will agree.
If you want me to love that character, make it so I would believe that! Make him funny, helpful, make him sacrifice himself for me. Write a romance arc. You can't just make me buy that my character loves him already. (Compare to how Bioware or CD Projekt Red games write romanceable NPC characters, much better than this)
Also, while there IS said romance sidekick character, they don't... do anything. They appear at the beginning, and they're there at the end, but they don't do anything in the story itself. What? They could at the very least provide some quips or advice about situations you find yourself in.
Also... this game could seriously use some music. In addition to Newgrounds Audio Portal, you can find free music on Freemusicarchive.org (remember to check the license), Incompetech.com and Freepd.com
I should give props for small improvements over Storm Shadow - rolls make slightly more sense since you can customize your character with traits and equipemnt, more like in a role-playing game - and you can restore HP. Which overall makes combat somewhat fun, and less of a chore. So good on you for that.
More generally, I think I would recommend that you stop trying to make epic RPG stories by cramming them into interactive fiction - instead, it's a better idea to try to write stories that usually work best in adventure game format - spy fiction, mystery/detective, romance, comedy, personal drama, horror, exploring mysterious empty worlds and piecing together what happened - that kinda stuff. Epic sci-fi fantasy battles are always going to look lacklustre in this genre. Similarly, it might pay off to have some actual puzzles.