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This is based on information we have learned in the show so far, covering the time before the exodus of Kobol up until the latest episode "No Exit."
4000+ years ago
Humans lived on Kobol (in harmony with the g0ds) - the birth place of us all. At some point the humans develop the Cylons (toasters first and then skinjobs?). The skinjobs develop resurrection technology while on Kobol.
4000 years ago
The skinjobs on Kobol leave in search of a new home - Earth, thus becoming the lost 13th Tribe. There reasoning for leaving is as of yet unknown (perhaps they went to war with the humans, lost, and were exiled - similar in ways to how the 12 Colony Cylons exiled themselves from the Colonies after the war ended).
On their way to "Earth" (I put Earth in quotes because we still don't really know if it is The Earth), the 13th Tribe stopped on the Algae planet and built in the "Temple of Hopes" aka "The Temple of the Five" and prayed for guidance. G0d (or g0ds, Ellen referred to their prayers being answered by G0d - but Sam claims that the toasters from the 12 Colonies developed the belief in a single G0d) answered their prayers and showed them the way to Earth.
2000-4000 years ago
The 13th Tribe find their way to and settle on "Earth." The 13th Tribe learn how to (or simply evolve the ability to) procreate on their own without resurrection technology. As such Cylon resurrection technology is lost/no longer needed. During this period the skinjobs create their own form of toasters (do they even know they themselves are/originated from machines?).
2000 Years ago
Exodus from Kobol. Both humans and the g0ds exodus from Kobol, the humans forming the 12 Tribes. As far as I know we haven't learned the exact reason(s) for this. From myths, legends, etc. on Kobol humans and the g0ds lived in harmony on Kobol until a great calamity of some sort occurred forcing the exodus. The exact timing of when the g0ds abandoned Kobol is also unclear, possibly before the exodus of the 12 Tribes. Though we do know that the g0d Athena, in her grief at the human exodus, commits suicide, thus at least one g0d stayed to witness the exodus. The 12 Tribes settled upon the 12 Colonies (Aerilon, Aquaria, Canceron, Caprica, Gemenon, Leonis, Libran, Picon, Sagittaron, Scorpia, Tauron, and Virgon).
At this same time the toasters on Earth rise up against their "skinjob" masters and start a devastating war that essentially wipes out all of Earth (as far as we have seen).
Prior to the destruction Tory Foster, Galen Tyrol, Sam Anders, Saul Tigh and Ellen Tigh all receive visions of some sort - Sam saw a woman, Tori saw a man, Galen thought he had a chip in his head, nobody else could see them (head jobs?) - warning them of the upcoming war. Together the five of them reinvent resurrection technology. While Tyrol does the majority of the leg work, Ellen comes up with the intuitive leap to make the technology work (organic memory transfer).
All five die on Earth but are resurrected on an orbiting ship and begin their sub-light (aka relativistic) speeds journey to the 12 Colonies; assuming that the humans there will eventually create their own Cylon toasters, and to warn them to treat them well and not enslave them, in the hopes of stopping the cycle of death and destruction.
60+ Years ago - 2000 Years ago
The Final Five cylons (in reality the first five) retrace the steps of their ancestors to determine the location of the 12 Colonies, visiting the Algae planet and the "Temple of Hopes" in the process. At sub-light speeds their journey takes thousands of years.
It has been hinted at, although far from confirmed, that the 12 human tribes upon settling the 12 Colonies had a major technological backslide (or even a whole societal backslide) and fell into a dark age even (again, not confirmed). Obviously, over the course of two thousand years the Colonies redeveloped technology, including the jump drive (which, according to Sam, did not exist - at least for the Cylons - before).
60+ Years ago (This information comes from the Promo information for "Caprica")
Daniel Graystone begins work on developing Artificial Intelligence. After the death of his daughter Zoe (due to the religious fanaticism of her boyfriend) he becomes intent on "resurrecting" her. Already having a digital copy, or clone, of her personality he uses stolen technology (from where?) to create a robotic version of his daughter - the first step towards creating the Cylon (cybernetic life-form node) race. In addition, Joseph Adama (William Adama's father) loses his wife and daughter from the same terrorist attack that claimes Zoe. Joseph Adama works with Daniel Graystone in bringing back their children, but is appalled at Daniel's methods and ethics. The events discussed here will be explored in much more detail in the upcoming prequel show "Caprica."
50+ Years ago
The first war between the 12 Colonies and the Cylon Centurions (toasters) breaks out when the toasters, tired of being enslaved by their human masters, rebel. The war last somewhere along the line of 12 years.
William Adama fights in the very last battle against the Cylons and discovers a laboratory on an icy planet where Cylons are experiments on humans, he also discovers the first hybrid.
40+ Years ago
The Final Five arrive at the 12 Colonies only to discover war has already broken out b/w the toasters and the humans.
Learning that the toasters have already begun work on skinjob counter-parts, and having only succeeded in creating a hybrid, make a deal with them. In exchange for ending the war, the Final Five will show the toasters how to create their own skinjobs. Ellen Tigh feels that this is a wise move because the toasters have developed a belief in a loving and compassionate G0d (the one true G0d), and thus the toaster, and in turn the skinjobs, will not want to seek revenge upon the humans.
The first of these new skinjobs created is John Cavil (1), followed by Leobon Conoy (2), D'Anna Biers (3), Simon (4), Aaron Doral (5), #6 (who thus far goes by many names, including Shelly Godfrey Gina Inviere, and Natalie), Daniel (7), and Sharon Valerii (8).
John Cavil turns out to be very vindictive, and rejects the ideas of mercy and forgiveness and wants to seek revenge upon the humans for enslaving his Centurion cousins. In a fit of jealousy he kills Daniel, the number 7 model, completely by corrupting the amniotic fluid that the #7 models grow in and the genetic code. In addition, Cavil traps the Final Five in a room and suffocates them, and before they can fully resurrects boxes them. Upon unboxing, he blocks their original memories and gives them false ones and slowly introduces each one back into human society, starting with Saul Tigh shortly after the first Cylon war ends. Cavil's reasoning for this is so that they (the Final Five) may get a first hand look of how humans really are.
4 Years ago
The Cylons (now skinjobs) return to the 12 Colonies, and in a sneak attack, wipe out virtually all of humanity, save for a small rag-tag fleet of some 50,000 humans.
The Final Five are not killed during this attack and thus John Cavil decides to "play" with them, and make them suffer until they are eventually killed and resurrect. He puts Ellen on a transport away from the Colonies that joins the rag-tag fleet. He plays resistance with Sam on Caprica. Eventually he takes Galen's confession and convinces him that he is not a cylon, he also tortures Tigh and rips out his eye. We do not currently know if he has done anything specific to Tory to mess with her head.
Gaius Baltar, unbeknownst to himself, is instrumental in the destruction of the Colonies as a result of giving a Number 6 Model full access to the Colonies defense mainframe. Upon escaping the destruction of the colonies, Gaius begins to experience a "head 6."
4 Years ago - 2 Years ago
The rag-tag fleet escapes the Cylons and begin a search for the lost 13th Tribe and Earth.
Laura Roslin becomes the new President of the colonies. She has terminal breast cancer.
Kara tortures a cylon model, Leoben, and is told by him that she is special and has a destiny.
Bill Adama finds Ellen Tigh amongst the ragtag fleet, and brings her to Galactica.
Baltar creates a Cylon detector, it shows that Sharon is a Cylon, but he hides the results. He uses the Cylon detector on Ellen (does he know she is a Cylon?). We find out though, through head 6, that "everyone passes theses days."
Along the way the fleet discovers Kobol and learns that any return to Kobol will be met with death. They also find the Tomb of Athena, showing them constellations as would be soon from Earth.
During this period Boomer/Sharon discovers she is a Cylon and attempts to murder Bill Adama.
Kara returns to the 12 Colonies, specifically Caprica, to retrieve the Arrow of Apollo.
On Caprica she finds Helo and another Sharon model whom Helo has impregnated and the resistance movement, led by Samuel T. Anders.
While on Caprica Kara is captured by the skinjob Simon, and learns that they are experimenting on humans and trying to figure out how they may procreate through biological means (currently the skinjobs can't have babies) as opposed to only surviving through the download process.
Kara, Helo, and the Sharon model leave Caprica to join back with the fleet.
Boomer/Sharon is killed and resurrect back on Caprica and must deal with her Cylon nature.
The fleet runs into another Battlestar, Pegasus, commanded by Admiral Cain.
A riff forms b/w the fleet and Pegasus upon learning of Cain's brutal tatics.
Galactica and Pegasus but problems aside, and ally with eachother to destroy the Cylon Resurrection Ship, thus preventing Cylons from resurrecting upon their death.
Cain is murdered by a #6 model, Gina, that was being held captive and continually tortured. Baltar helps Gina escape.
Roslins cancer is cured by using the blood of the yet unborn child of Helo and Athena.
Helo and Athena's baby is born, Hera - the first human/cylon hybrid, the future of things to come.
Roslin arranges so that the baby is taken from Helo and Athena, and given to a woman Maya to be raised. Helo and Athena think that the baby has died.
On Caprica, Boomer and Caprica 6 (the 6 that seduced Baltar and brought down the Colonials defenses) start a movement within the Cylons to abandon the 12 Colonies - they had made a terrible mistake in trying to wipe out humanity.
Kara, with the help of Cylon jump technology (as given to them by Sharon/Athena) returns to Caprica to rescue the resistance movement there. Upon arriving they find the resistance, and learn that the Cylons have abandoned the Colonies (as told to them by Cavil).
At the same time, New Caprica is discovered.
Gaius Baltar is elected President and orders the fleet to settle upon New Caprica, because it is hidden from the Cylons.
Brother Cavil takes Galen Tyrols confession, and convinces him he is not a Cylon.
Gina, deciding to finally commit suicide (fully and completely with no way of resurrecting) sets of a nuclear blast in the space around New Caprica, destroying herself as well as several thousand other humans.
Kara and Lee have a major falling out when Kara marries Sam. Lee in turn marries Dualla.
Tyrol and Cally get married, Cally gets pregnant with Tyrol's son (though we later find out that it is actually Hot Dog's son)
2 Years ago - Present
Humanity has settled on New Caprica, life is difficult, Gaius is a horrible President.
The Cylons appear, having detected (a light year away) the telltale signs of a nuclear explosion. What remains of the fleet in orbit, jumps away (including Galactica and Pegasus).
The Cylons occupy New Caprica, and a resistance against them is formed. The Resistance consists of many people, most notably the Final Five, Saul Tigh is the leader.
Cavil tortures Tigh and takes one of his eyes.
Tigh murders his own wife Ellen for betraying the Resistance to the Cylons.
Bill and Lee come up with a plan to rescue the people off of New Caprica. Humanity escapes the Cylons yet again from New Caprica, Pegasus is destroyed in the process.
Upon escaping, Gaius chooses to go with the Cylons instead of humanity, as he knows they all hate him.
Maya is killed during the escape from New Caprica, and thus the Cylons take Hera back to their fleet.
Ellen resurrects aboard a baseship, and is met by John Cavil, who holds her captive.
The fleet discovers a beacon in a Nebula left by the 13th Tribe.
The fleet, running low on resources, finds the Algae planet to replenish their food supply.
Tyrol discovers the Temple of the Five on the Algae planet, which supposedly holds the "Eye of Jupiter", another marker on the way towards Earth.
The Cylons show up, demanding the Eye of Jupiter, as they have decided to settle on Earth.
Athena and Helo learn that Hera is actually alive, and is on one of the Cylon baseships. Athena goes to the baseship and gets Hera back. The Eye of Jupiter turns out to be a supernova.
D'Anna Biers upon seeing the faces of the Final Five during the Supernova is boxed by Cavil.
Helo notices that a painting in Kara's apartment on Caprica is eerily similar to some markings inside the Temple of Five.
Gaius Baltar returns to the fleet.
Kara is killed when her Viper is destroyed in a gas giant, she believes she was chasing after a Cylon Heavy Raider.
Gaius is put on trial for his crimes, Romo Lampkin and Lee Adama represent him. During the course of the trial Lee resigns his position from Galactica. Gaius is found innocent.
Roslins cancer returns.
Tory, Sam, Tigh, and Tyrol all hear the same song (All Along the Watchtower), and suddenly realize that they are all Cylons.
Upon jumping to the Ionion nebula, the entire fleet loses power simultaneously. The Cylons show up as well. Lee, although no longer a Viper pilot, gets in a Viper to protect the fleet - only to discover Kara Thrace in a seemingly brand new Mark II Viper in the Nebula.
The Cylons retreat when the Raiders scan Sam (who is flying a Viper) and determine that he is one of the Final Five.
Gaius, a free man with no where to go, is taken in by a cult of followers who believe him to be a prophet of sort. Baltar takes on the role and preaches the belief of the one true G0d.
Tory, Tigh, Sam and Tyrol keep their new Cylon identities a secret.
Tory murders Cally, when Cally discovers that the four of them are Cylons.
Kara claims she has visited Earth and knows has to get back there. We do not yet know how or why Kara came back to the fleet.
Kara is given a ship to look for Earth.
During the search a mutiny almost occurs on Kara's ship, Sam shoots Gaeta in the leg - Gaeta ends up losing his leg.
In addition they run into a damaged Cylon Baseship, and learn that the Cylons have entered a civil war - The 1's (Cavil), 4's (Simon) and 5's (Doral) against the 2's (Leoben), 6's and 8's (Sharon). The rebel Cylons along with Kara and her crew return to the fleet.
The rebel Cylons with help from the Colonials enact a plan to destroy the Cylons Resurrection Hub, thus preventing Cylons from ever resurrecting again, essentially becoming mortal.
During this time, D'Anna is unboxed by the rebel cylons and brought back to the colonial fleet.
D'Anna knowing the identities of the Final Five, demands there return. Tigh comes forward and admits who he is, Tyrol and Sam follow suit. Tory manages to make her way on to the Cylon baseship.
Tyrol and Sam, before coming forward, are drawn to Kara's pristine Viper. Kara suddenly discovers a signal that the Viper is picking up - it is coming from Earth.
The Colonials and the rebel cylons decide to ally and jump to Earth.
They arrive at Earth, only to discover that it is a desolate wasteland.
Tyrol, Tory, Sam and Tigh begin to have visions of their lives on Earth. Dee commits suicide upon the discovery of a ruined Earth. Tigh has a vision, and realizes that Ellen is the final cylon.
Gaeta gets trapped aboard a Raptor with a Number 8 he knew on New Caprica, He learns that this 8 betrayed him in a very personal and horrible way.
Gaeta is rescued and returns to the fleet and is dismayed upon learning of the fact the Adama plans to install Cylon FTL drive in all ships in the fleet. Gaeta, no longer trusting of Adama, feeling that he is unwisely creating an alliance with the Cylons, mutinies. With the help of Tom Zarek, Gaeta succesfully takes over Galactica. Roslin escapes to the Cylon baseship. Lee and Kara, Tigh and Adama and a number of other people fight to regain control of the Galactica, they succeed. Gaeta and Zarek are executed.
During the mutiny, Sam is shot in the back of the head.
As a result of being shot in the head, Sam begins to remember everything, his time on Earth, everything and begins to relay that information to Tory, Tigh and Tyrol.
Ellen escapes the Cylon baseship that she is being held captive on, with the help of Boomer.
Questions still unanswered
Based on this timeline and what we have learned, these questions still remain unanswered:
What is Kara Thrace, how did she "resurrect" and get back to the fleet? In what time period did she visit Earth?
What is Head Six/Head Baltar?
What/who are the g0ds of Kobol?
Why did the Cylons leave Kobol long before the humans left?
Why did the humans leave Kobol?
What happened to the g0ds?
Is the Earth the fleet found our Earth? If so, is this in our past or future?
Who/what is the Cylon g0d aka The One True G0d?
I'm sure there are more questions that I am missing, but that's all I can think of right now.
Did Baltar know that Ellen was a Cylon when he ran the Cylon detector on her?