I can't really go into a lot of details, but I recently had a chance to read a copy of the scripts for the final two episodes of BSG. It's conceived as a two-part series finale, which Ron Moore penned himself around the time they went into production on season one. He may not have had a detailed five-year plan like JMS did with B5, but I like that he always knew where he was going.
I couldn't take the scripts with me, and didn't have all that much time, but I was able to commit the final scene to memory. Obviously, these are massive spoilers.
To give you a little context, in the penultimate episode, the fleet follows the final two signposts to Earth. First, they end up at (I think) Proxima Centauri and a barren planet the fleet originally mistakes for Earth. They realize their error and find the final clue to Earth's location. In the final scene of the episode, Sharon's Raptor jumps behind the moon. Just as she's about to leave in frustration, she sees Earthrise.
In the finale, Roslin and Adama decide that Earth's not ready to know the truth yet, so they're going to assimilate into the culture, quickly advance our scientific and technological knowledge, and then make themselves known. The goal is to prepare Earth for the coming of the Cylons without causing widespread panic. Colonists are provided forged documents and are surreptitiously ferried to the surface. The fleet is left outside the solar system, and one Raptor is secreted in a cave.
Here's the final scene:
EXT. SPACEPORT - DAY
Title: Twenty Years Later
SLOW PAN AND ZOOM FROM LONG TO MEDIUM SHOT, FINALLY SETTLING ON A SMALL, OLD FAST FOOD RESTAURANT SITTING AT THE EDGE OF THE SPACEPORT, IT'S WHITE BLOCKY EXTERIOR FAMILIAR TO MILLIONS.
INT. WHITE CASTLE - DAY
ADAMA, NOW A VERY OLD MAN, SITS ALONE AT A TABLE, FOOD IN FRONT OF HIM. THE DOOR OPENS AND A FIGURE IS SILHOUETTED IN THE SUNRISE. ADAMA LOOKS UP TO SEE NEIL PATRICK HARRIS WHO SEES ADAMA AND WALKS TOWARD HIM, SMILING.
Admiral Adama. It's a pleasure to finally meet you.
Do I know you?
No, but I know you.
Son, I'm just trying to enjoy my breakfast. Can I help you with something?
I am God.
I am God. (BEAT) I was the first sentient Cylon.
ADAMA TRIES TO RISE BUT NPH PUTS A HAND ON HIS SHOULDER AND GENTLY PUSHES HIM DOWN
We've prepared these people for you. You won't take Earth with a surprise attack the same way you destroyed our homes. There is no Balthar here to betray us.
I'm not here to destroy you, Adama.
Then why are you here?
I'm here to apologize. And to buy you breakfast.
Apologize?! You destroyed our homes, killed our families, and chased us across the galaxy. And now you want to apologize?
Yeah, it was a dick move on my part. That's why I'm paying for your meal.