Current use of Bad Guys story arc in the Script Outlines:
Episode 1: The Awakening of the Elves
(1) The episode opens with Elwë and Celeborn fleeing from the Dark Rider, who is revealed to have been taking elves.
(2) Optional: Mysterious cloaked stranger watching the meeting discussing the Dark Rider? Melkor or Sauron?
Episode 2: The Ambassadors
(1) In Valmar, they meet Nienna, who asks Ingwë about his loss. He explains how his wife was taken by the Hunter, and Nienna grieves with him.
(2) To answer their questions about the War, Aulë takes the Ambassadors to the Courtyard of the Halls of Mandos. Aulë explains to them about the war and Melkor, and that Melkor is chained inside.
(3) In Cuiviénen, Morwë is telling stories to some Quendi children as Míriel watches. He tells them about Oromë's arrival, hinting that he was the Dark Hunter and how he took away Ingwë, Finwë and Elwë, "...and they were never seen again." Míriel angrily shouts at him to not tell that story and that "They're coming back!"
Episode 3: The Great Debate
(1) The Dark Rider returns to Angband. Mairon (now Sauron) and Gothmog argue about their different plans for the captive elves: Gothmog wants to kill all the elves, he is dismissive of whatever Sauron's plan is (he never gets to articulate it) as unnecessary and over complicated. Sauron is snarky and sulky in response - he is outgunned in Angband by Gothmog and his balrogs.
(2) Eöl notices a large bat as he storms away from the Debate.
(3) Spy!Thurengwethil returns to Angband, and we check in with Sauron and Gothmog. Sauron reveals to her his motivation for working with the elves - why destroy what you can cultivate?
Episode 4: The Great Journey
(1) Mairon visits the dungeons, and chastises Tevildo for his harsh methods. "They're no good to me dead" type of complaints, and that Tevildo is pushing them too hard. Sauron shows him how it is done, and brings an elf in for a 'good cop' interrogation. He wipes away the blood, tells him it doesn't have to be this way, and starts preaching the cult of Melkor. The elf is obviously terrified of Tevildo (who is prowling in the corner), but responds hesitantly to Sauron's overture.
Episode 5: A Touch of Destiny
(1) Balrogs have gone elf-hunting, and are picking off some of the Teleri who fled from the storm into the woods in the opening scene. Some run away across a river, and the balrogs move to pursue. Uinen rises up out of the river, and we get to see what a wet balrog looks like. Balrogs make a strategic retreat and return to Angband. We see Thuringwethil watching.
(2) Sauron in his mad-scientist workshop, tinkering on proto-werewolves. Thuringwethil comes in to check on him. He asks her what the balrogs are up to, and if they know about his project yet. She confirms that they're still in the dark.
Episode 6: Elvenhome
(1) Confrontation in Nan Elmoth. Wolves show up and attack search party, disperse when Melian and Elwë emerge, Melian helps one of the injured. Thingol and Melian become king and queen of the Sindar.
(2) Final Angband scene (Draugluin walks in to report, Sauron in the middle of creating an orc, etc)
As you can see, we start with the Dark Hunter fear and the disappearing elves for the first 2 episodes, and then introduce the Angband characters in Episode 3, showing the power dynamic and how Sauron is bottom rung and frustrated. We then gradually get through some elf-torture and werewolf-development, showing that Sauron wants to build his own army, separate from Gothmog. Thuringwethil is a spy who wants to know all the secrets...she realizes that Sauron has ideas and is curious about them. We then leave them all to their own devices for awhile, so orc creation will remain (mostly) super secret, but all of the ingredients are in place for Melkor's return, Gothmog's right-hand-man spot, and the final touches on the orc project being delivered by Morgoth, who will unleash these creatures on Middle Earth.
I realize there is some concern that completely dropping these characters in Episode 6 and not picking them up again until Episode 13 might be problematic, but keep in mind that we're dropping Thingol and Melian and all of the Sindar until next season.
We do have the opportunity to glimpse Middle Earth through the palantíri if we need to use that as an excuse to go back in the second half of the season. But those episodes work fine without being interrupted by this.