How would I end it?
How will the two part final episode go down? There are many good possible predictions, but nobody on the outside truly knows.
But given the constraints that the ending is sad and dark, here's how what I would want to see. Not what we necessarily will see.
- The Final Five will die, in the course of saving humanity and uniting humanity and all the Cylons except probably Cavil. This is a classic rule of tragedy. They had good intentions, but spawned evil in spite of them, and so they will die making it right.
- There is not enough time for the "string puller" to appear as an on-screen character, but...
- The string puller will provide some expository explanation of things, speaking through head characters to everybody who has had a head character. She will announce who she really is. Baltar will see her has a Six. Six will see her as a Baltar. Roslin will see her as an Elosha. Starbuck will see her as a Leoben and/or her father. Adama will see her as the first Hybrid. The Final Five will see her in the form of the messengers they saw 2,000 years ago.
- Most of it will be shown as a Six explaining things to Baltar, but interspersed will be clips of the same story being told to the others.
- Baltar and Caprica Six will work together with the Final Five and create a computer virus which infects the ships of Cavil's factions to disable them. In addition, this virus will remove the inhibitors from Cavil's centurions. This will help redeem Baltar for his role in allowing such a virus to be inserted into colonial systems.
- One of the Final Five, Sam, will pilot the Galactica against Cavil's forces and crash it into them. This may play a role in planting the virus, which may be done by the others in the final Five.
- When Ellen goes out on her suicide mission to recruit the Simons and Dorals, Bill says to Saul, "It's too bad she won't live. But then again, who does?" (Ok, not really.)
- For added irony, the lobotomizing of the raiders should interfere with their ability to defend the Colony. (Though not too ironic as unlobotomized raiders would not attack the F5.)
- Baltar lives because he needs to play a role in saving Hera and raising her to be the first of the joined generation.
- Athena and Helo die. But before they do, they become convinced either by virtual beings, or by the Final Five, that it is god's plan that Baltar and a Six raise Hera.
- Boomer dies saving Hera from Cavil and getting her partway out.
- The head-beings explain who the Lords of Kobol were, and what happened when the 13th tribe was expelled, and when the rest were expelled 2,000 years later. Their fate may be revealed.
- The head being reveals that the Lords of Kobol were once humans on the ancient homeworld of humanity who developed A.I. and elevated themselves to godlike status. They took their Children with them and settled on Kobol after a man-machine war, and lived with a paradise among them. The String Puller herself was a woman on the ancient home. Her DNA, in archives has been re-used from time to time, most recently by the Final Five to make one of the 8 Cylons they made.
- She reveals that even the humans are artificial, though much closer to original humanity than the Cylons. Starbuck had to die and be recreated to show them that even humans like her are children of God.
- The Simons and Dorals, given the full scoop about their creation by the Final Five, rejoin with the rebels. Cavils are mostly killed by Centurions and fleet forces. All Cylons and humans are now united.
- The String Puller reveals that this union was the goal of all the troubles and mysteries. She appears to Starbuck as her father and shows them the way to a new, blue planet. Roslin dies in orbit over the planet.
- The fleet settles on the planet. It is the real Earth. On it are ancient ruins of the Pyramids, Mt. Rushmore, New York, all destroyed for many thousands of years, but the planet is inhabitable. The date is revealed. A.D. 8,000.
- Baltar and Six will raise Hera, along with the combined and united Cylons, Centurions and humans, who vow to make more like her and end the Cycle.
- Cut to a street in New York. A.D. 2009. We see a Six, but slightly different, in her red dress. She has just receieved her PhD in Artificial Intelligence. She's out on the town, celebrating. She purchases a copy of Electric Ladyland by The Jimmy Hendrix Experience. She smiles.
(As noted, some of the things here are based on constraints and information that has leaked out. I would not do the final scene in New York that way, and I think making Baltar in charge of Hera doesn't make a lot of sense but it's been predicted so much, which means Helo and Athena have to die.)