One more note on the ominous implications of the Cipher Hunt. I personally think that right now Alex is having fun being spooky and ominous, going “ooooh, Bill is still hanging around…he might be RIGHT BEHIND YOU! MWAHAHAHAHA!”
It’s like the pre-ending jumpscare in a horror movie where the monster you thought was dead opens its eyes. It’s not about changing the ending for the characters so much as giving the audience the lingering feeling of “oooh, this creature is still out there somewhere.”
We may never get a canonical explanation for why Stan was singing “we’ll meet again,” or how the Cipher Hunt even fits into canon (if it does at all.) Alex knows his fans are going to run wild with speculation, theories and fan content, and that’s all just part of the fun! But none of it undoes the happy ending we did get in canon. It’s all just a bonus for people who enjoy the speculation.