Which characters do Threads of Fate plot rule apply to?
Based on rulings from Simon Lundström (who translated the rules), as stated here:


  The subplot says (or should say) "characters who had at least one goodwill at the end of the previous loop".


So only the characters (including corpses) who had a Goodwill counter on them at the end of the loop get 2 Paranoia on them at the start of the next.