How Battlestar Galactica Should Have Gone
Minor tweaks to the very end keep all the major dramatic twists without destroying the message otherwise built up throughout the series.
To make this tweak work, it must be established earlier in the series — through peripheral dialogue, not yet immediately relevant to the plot — how the Colonists' and Cylons' jump drive technology works.
The jump drive is theoretically capable of instantaneous transportation of an object between any two points in spacetime, no matter how distant. However, the vast majority of possible jumps terminate in massive objects such as black holes, stars, or if you're very lucky, just the core of a planet. The difficulty in performing a jump, then, is in calculating a jump trajectory that does not drop the ship into such an object upon its re-entry into normal space. For the obvious reason of there being more possible obstacles to intersect in between, it is usually easier to calculate a jump trajectory to a nearer point in space than to one further away.
For other reasons unnecessary to specify, it is easier to calculate a clear jump trajectory to more distant points in the future of the origination point than to points nearer to the present, and it is impossible even in theory to calculate a clear jump trajectory to points prior to the present. (Although such trajectories may exist, we cannot determine what they are, and they will, like all clear jump trajectories, be a tiny minority of possible jump trajectories). A more practical limitation is that this calculation itself takes time, during which the origination point is changing and thus the calculations are becoming less accurate, and besides which, you are approaching your intended destination time the slow way already without making any reduction of the distance between you and your destination location.
This dependancy on calculation for jump travel is why Cylon ships are "faster" than Colonial ships: the Cylons, being machines, are far more proficient at completing the necessary sensor scans and crunching the requisite numbers to accurately determine a clear jump trajectory to greater distances at nearer times, allowing them to jump further faster than Colonial ships. Discussion of this fact of faster Cylon travel, already established in the BSG canon, is probably the best opportunity to detail the workings of jump drive in an off-hand way.
With that now established, the changes to the actual plot of the ending can take place.
The first significant plot change is to have more about the downfall of Kobol discovered when Galactica visits it. Let it be established that two thousand years after the original expedition to find Earth (the "Thirteenth Tribe") departed Kobol, the humans of Kobol developed cybernetic servants much like the later Cylon Centurions, which likewise rose up against their masters on Kobol. In the ensuing war, Kobol was rendered uninhabitable, but the proto-Cylons were destroyed; the Twelve Tribes then scattered in search of new habitable worlds and eventually became the Twelve Colonies of Kobol. Upon discovering this news, the unknowing Five amongst Galactica's crew once more are beset with the sense that "all this has happened before", as they were when Twelve Colonies first fell. But learning that the Thirteenth Tribe departed well before the fall of Kobol renews hope that they may be of aide against the Cylons pursuing the Colonial Fleet.
However, when Earth is finally discovered in the final season, it is (as in canon) a desolate wasteland, uninhabitable, destroyed by a nuclear holocaust of its own around the same time that Kobol was two thousand years ago. However, investigation reveals that the civilization on Earth is much more than four thousand years old, and furthermore, that the inhabitants of it were (as in canon) of humanoid-Cylon biology. Wandering the ruins, the (now-known) Five remember what happened to their civilization; they were the descendents of the creations of the original human civilization, which developed here on Earth. Their kind had, long before the Five's time, come into conflict with those first humans, and after their victory in that war, driven the humans away from Earth. Many thousands of years later, a war fleet of those humans returned from the new home they had found in the stars, and brought destruction to the humanoid-Cylons of Earth, destroying themselves in the process. But the Five had reinvented the Resurrection technology with which their kind were first created, and using it, survived the destruction of Earth, before seeking out the new homeworld of mankind to make amends with their creators.
When Ellen, the last of the Five, is recovered later in the final season, the rest of this story is unveiled. Arriving, after a long and arduous journey of many thousands of years, at Kobol, the Five found that mankind there had repeated the same mistakes, and destroyed their world in a war with their creations. But eventually, to their joy, they discovered the Twelve Colonies... only to find them, to their dismay, in the midst of repeating the same mistsake again! Promising the Cylon Centurions more advanced, humanoid forms if they withdrew from their attack on the Colonies, the Five helped engineer the eight main lines of the modern Cylons, only to be betrayed by the Number One line and placed amongst the Twelve Colonies to witness their destruction and be "taught a lesson" before resurrecting, as in canon.
Now, after the surviving humans of the Twelve Colonies and the rebel lines of the humanoid Cylons have at long last made peace between each other, there is only the problem of the remaining enemy Cylons to deal with. As in the canon finale, the combined Fleet is to rally at a preset location, while Galactica travels to the Colony, the ship which the Five travelled back from Earth in, and the base of the enemy Cylon operation under the command of the Number One line. These events unfold just as in canon, until the final moment when the Colony is falling into the black hole it orbits and Galactica is being pulled in with it. This is where the pre-established operation of the jump drive comes into play.
Adama orders Starbuck to jump the ship out of there, but the jump computer is offline. He orders her to jump them somewhere anyway, punch in any coordinates at all manually and just get them the hell out of there. She protests that a random jump will in all probability jump them into the middle of a black hole. Adama counters that if they don't jump then they are certainly going to end up in a black hole — this one, that they're falling into right now! Swayed by that impeccable logic, she thinks of numbers to enter into the computer; and the numbers she translated out of the mysterious music which she and the Five have been hearing — the music which awoke the Five's memory of their identities, and later their history, which lead Starbuck to Earth and back — is the first things that come to mind. She enters those figures, engages the jump drive, and Galactica vanishes.
It reenters normal space high in the atmosphere of a planet, freefalling toward it; a very near collision, but still technically a clear jump path, against all odds! Nevertheless, the ship is broken by this last jump, as it was previously established it would be before they even engaged in battle with the Colony. Starbuck and Adama manage to stabilize their descent enough, and "land" the ship as softly as possible in one of the planet's oceans. The few crew who remained on Galactic and survived the battle grab whatever they can carry and abandon ship in Raptors and other small ships, as Galactica sinks to the bottom of the sea.
Now stranded on this strange and thankfully quite habitable world, they attempt to use what little technology they could salvage from Galactica to determine their location and send out some sort of beacon to the rest of the Fleet at the rendezvous point. Stellar positioning indicates that they are still in the nearby vicinity of Earth, the Colony, and the rendezvous point, which should put them easily within range of a beacon signal. But after failing to make contact with the Fleet after some time, they are baffled; until they encounter a tribe of primitive humans, and realize that they are not merely somewhere in the vicinity of Earth, they are on Earth, some unknown many thousands of years prior to their own time. Their random jump took them back in time to the beautiful home they were looking for all along. Several people remark how unbelievably improbable this is. Baltar essentially chalks it up to "God Did It". And Starbuck vanishes into thin air when everyone's backs are turned.
Meanwhile, in the future, the combined Human-Cylon Fleet waits at the rendezvous point well past the scheduled time. Eventually scouts are sent to the black hole where the battle with the Colony took place, but nothing is found there but the black hole itself; any evidence has been consumed by it. After scouting and searching for beacons or any sign of survivors of Galactica or the enemy Cylons, the combined Fleet departs together for points unknown in search of a new home, mankind and their creations united in peace at last.
The stranded crew of Galactica on ancient Earth do what they can to teach and uplift the primitive humans, planting the seeds of what would become some of Earth's great ancient civilizations, and long after their deaths being remembered as gods. Many, many thousands of years later, when modern humans have begun to develop robot technology for the first time again, the "Virtual" Baltar and Number Six who have appeared to their respective counterparts observe our progress, and remark on how all this has happened before, and all this will happen again, hinting ever so slyly in their dialogue that they are somehow the ascended descendants of the combined Human-Cylon Fleet which this entire circle of events, which they have helped ensure, has created.