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Many Years Ago:

The Cetra, a nomadic magical race which may or may not have originated on the Planet, settle after a long and arduous journey. Some Cetra (later known as Ancients) choose to continue their journey, whilst others settle down and eventually become humans. A few true Cetra still survive, however. [FF7]
The Cetra create a tablet describing the existence of Chaos and Omega and their purpose. This tablet will be discovered by Dr. Grimoire Valentine and Dr. Lucrecia Crescent, providing the spark for their experiments. [DoC]
2000 Years B.G.:

JENOVA, a malevolent creature, crash-lands on the planet and causes a huge rift, the Northern Crater. JENOVA infects the Cetra with a virus, turning them into monsters. Most of the remaining Cetra are slaughtered as the humans hide out in their new settlements, avoiding the terror. The Planet creates five Weapons to battle JENOVA, but they are never used. A small number of surviving Cetra succeed in containing her in the Northern Crater. The Planet begins to heal itself using its life energy. (It never fully heals.) [FF7]
Between 1999 - 41 B.G.:

The Shinra Electric Company emerges as the leading energy provider in the world. They use Mako energy, which is drawn from the bowels of the earth. Mako is also known as Lifestream, a spirit force which is shared by the planet and everyone living on it. Condensed Mako, known as Materia, draws a high market for its magical properties. Eventually Shinra diversifies into military, political, urban development, scientific, astronomical, and communications departments and becomes known as the 'Shinra Corporation', or simply 'Shinra'. [FF7]
The existence of Shinra gives way to Midgar, the city constructed around the central power plant. Eight Mako Reactors are placed at the edge of the circular city to provide power to the two levels: the upper plate consists of the well-to-do society, and under the plate, where the slums are.
Knowing the Mako can't last forever, Shinra begins conducting a search for the rumored 'Promised Land', a land of supreme happiness and abundant Mako. Only the Ancients know of its location, and Shinra intends to build 'Neo-Midgar' there. [Conjecture: in DoC, Dr. Valentine mentions the ancient tablet may contain info regarding 'Promised Land', so we can assume they are already looking for it at this point.]
The Turks are formed as an internal and hush-hush departement in Shinra; they carry out less desirable missions like kidnapping and assassinations. [FF7]

29 B.G.:

Vincent Valentine is assigned to protect Lucrecia Crescent while she is working with Dr. Hojo, a brilliant Shinra scientist. He does not know his father was working with Dr. Crescent before he died. [FF7 and DoC]
Vincent falls for Lucrecia, but he also sees that she is in love with Hojo, and resigns himself to that fate. Lucrecia also chooses Hojo and his proposed experiment on her unborn child. She does so because she feels guilty about Vincent's father. Vincent discovers this fact, and additional information about the experiment that killed him. The effects of this on their relationship are unknown, but there is strife. [FF7 and DoC]
28 B.G.:

Lucrecia's son is born and given the name Sephiroth. He is not told his true origins, however, instead being told that his mother, named Jenova, died giving birth to him. [FF7]
When Vincent discovers that Sephiroth is a result of Hojo having injected Lucrecia's yet-unborn baby with JENOVA's DNA, Vincent loses it and confronts Hojo. Hojo kills Vincent and conducts an operation on his body, reviving him and turning him into an unstable monster capable of mutating further when angered. [FF7 and DoC]
However, Vincent's body proves unstable, and Lucrecia takes it to perform further experiments on it. She injects Vincent with the Chaos gene; the process unleashes Chaos for a moment, but it is quickly subdued. She takes the Protomateria and embeds it in Vincent's body, fully reviving him but leaving him with the effects of both Hojo's experimentation (the ability to turn into monsters) and the Chaos gene. [DoC]
A short period later, Lucrecia dies, though her induction of JENOVA cells seems to have some sort of after effect. Vincent remains ignorant of her fate. In disgrace, Vincent enters a coffin in the Shinra Mansion and falls into a deep sleep. A "reflection" of Lucrecia remains inside a crystal in the Waterfall Cave.[DoC and FF7]

c. 15 B.G.:

Shinra's military wing proceeds to declare war on Wutai, an Oriental village. Shinra is eventually victorious, and its leader Godo humbled. Eventually Wutai loses its status as an honorable and polite nation and becomes a tourist attraction. [FF7]
Ifalna somehow manages to take Aerith and escape Hojo. Gravely injured, she makes it to the Midgar Sector 7 Train Station before collapsing. A woman named Elmyra discovers them, and promises they dying mother to take care of Aerith, as her own husband had died during the Midgar-Wutai war. Ifalna gives Aerith the White Materia, a legendary stone which has the power to call Holy. Aerith grows up thinking the Materia doesn't do anything at all. [FF7]
Over time, Aerith begins to show a strange talent. She is able to sense the death of Elmyra's husband out at war with Wutai before Elmyra actually gets word of it. She also seems to be able to 'talk to the Planet'. [FF7]
Eventually she gathers the interest of the Turks, who watch her, trying to persuade her to join their ranks. Aerith takes up a job as a flower girl in the Midgar slums. Tseng is appointed (or takes upon himself) the job as her watcher.[FF7]
Cid Highwind, creator of the Tiny Bronco biplane, is given the go-ahead by Shinra to launch a space rocket from his home town. Having looked forward to this time for ages, his excitement is mounting when his assistant, Shera, discovers a malfunction in an energy tank. She refuses to leave the soon-to-be-burning-hot chamber, and Cid forces himself to shut the rocket down before it can ignite. He refuses to forgive Shera for destroying his dream, and Shera lives with him in penance from then on, acting as a servant. [FF7]
15 - 10 B.G.:

Hojo performs experiments using cells from the body of JENOVA. He infuses Shinra soldiers with JENOVA cells. The results are staggering - those who are infected have strength and skills far beyond normal persons. Based on these results, Shinra forms SOLDIER, a program designed to use and train an elite military force by infusing subjects with Mako and JENOVA cells. [FF7]
Sephiroth quickly rises in the ranks of the Shinra military, due to his being the prototype for the SOLDIER program. He is monitored continuously and shows promise far beyond anyone else. [BC and FF7: It's hard to say what Square means by prototype, as FF7 says SOLDIER was created well after Sephiroth was born, and that Sephiroth was part of the JENOVA project, but BC says Sephiroth was the SOLDIER prototype. We may assume that by Prototype, they could mean role model, or the SOLDIER program was simply not officially introduced until after Sephiroth had been deemed a success.]
This is also the earliest mention of the Turks, which are technically known as the Investigation Division of the General Affairs Department in Shinra. [BC]
Cloud and Tifa grow up next to each other in the city of Nibelheim. They are not particularly friends, however much Cloud would like it to be otherwise. After the death of Tifa's mother, she runs into the Nibel Mountains. Cloud follows her, but a bridge they both stand on breaks, and Cloud is blamed for the injuries suffered by Tifa. They later have a conversation by a well where Cloud tells Tifa of his desire to go to Midgar and join SOLDIER, and promises to come back for Tifa if he should make it big in Midgar. [FF7]
Hojo brings his experiments to the Mako Reactor in Nibelheim, which involve dousing human beings in condensed Mako. Eventually the humans become completely unrecognizable monsters, but they are watched closely in sealed containers. The suspended-animation device containing JENOVA is moved there as well. [FF7]

5 B.G. (events of CC):

Zack and Angeal train together. Zack's sword is broken by a VR Sephiroth, but is saved by Angeal before he comes to harm. [CC]
Zack is summoned to SOLDIER Director Lazard's office and asked to investigate Genesis's disappearance in Wutai. Lazard says he will come along as well. Sephiroth is sent to the same place in a separate but parallel mission to finish the Wutai war. [CC]
Zack beats off Wutai troops, but is attacked by Genesis copies. Angeal stays to fight them while Zack takes Lazard to safety. When Zack comes back, the copies are dead and Zack is attacked by an Ifrit summon. Sephiroth arrives to save him. Apparently at this point, Genesis meets Angeal and convinces him to join him. [CC]
Genesis travels to Banora with his army, apparently to exact revenge on his parents, who he possibly believes are not his real parents, and accuses them of "betraying" him. He slaughters his parents as well as many other townspeople. [CC]
Rufus Shinra is appointed Vice President of Shinra. [CC - mail]
One month passes. Angeal arrives in Banora, meets his mother, leaves his Buster Sword with her and leaves the town. [CC]
Searching for Genesis, Lazard asks Sephiroth to investigate Banora. Sephiroth refuses, not wanting to fight his friends, so Lazard instead asks Zack and Tseng to go. They are attacked by Genesis clones while searching. Zack finds Gillian in Angeal's house. Tseng tells him that the Genesis copies have their headquarters in a factory on the outskirts of town, so Zack infiltrates it. He finds Genesis and Angeal there; Angeal follows Genesis and escapes. [CC]
Tseng informs Zack that Shinra has ordered an airstrike to obliterate Banora. Zack rushes to Angeal's house to attempt to rescue Gillian, to find her already dead with Angeal and Genesis next to her. Though Zack thinks Angeal killed her (and Angeal makes no attempt to dissuade him of the idea), in truth she committed suicide. Genesis summons Bahamut to attack Zack, and flies away on his one wing. Tseng rescues Zack with a helicopter, and Banora is destroyed by the Shinra air attack. [CC]
Shinra declares an end of the war with Wutai. Sephiroth is credited with achieving this goal and is lauded as a hero. [CC - mail]
Hollander begins experimenting with Angeal, realizing that his cells can be infused into monsters. They begin creating "Angeal copies". [CC]
Lazard calls Zack into his office to inform him that he's been promoted to SOLDIER 1st Class. He also asks him to go with Sephiroth to terminate Genesis and Angeal. Before he can reply, an alarm sounds - Genesis's army is attacking Shinra headquarters. Zack and Sephiroth fight the enemies inside the building and head out to Sector 8. They meet Tseng, Reno and Rude fighting off Genesis copies. Zack meets Cissnei for the first time, also part of the fight. [CC]

Director Lazard disappears, joining with Hollander. At some point, he submits to an experiment. Hollander injects him with Angeal's cells, turning him into a direct copy of Angeal. Unfortunately, he begins decomposing just as Angeal did. [CC - timing is a guess]
Zack is given a well-deserved vacation in Costa del Sol. The Turks are sent to keep an eye on him as well, ostensibly on their vacation (though Tseng refuses to wear a bathing suit). The vacation is cut short when Genesis clones attack. The forces begin attacks all over Shinra's area of control, including Junon. Lazard is behind the attacks, in an attempt to free Hollander. Zack heads over there. Hollander does indeed escape. Zack chases after him, but is foiled by the Genesis copies. Sephiroth finally shows up and tells Zack that Midgar has also been infiltrated by Genesis copies, including Sector 5, and that Zack has permission to go there.[CC]
Zack finds a malfunctioning Shinra attack machine (commissioned to fight Genesis copies) threatening Aerith; however, she is saved by an Angeal copy resembling a gryphon. The gryphon looks hurt, and stays in the rafters. Zack and Aerith finally make the flower wagon they'd decided on earlier, and begin selling flowers. In a scene in the church, Aerith writes down her "23 wishes" to Zack (actually 1 wish - to be with Zack more often), and he keeps it so he'll remember them. They have a good time together, but Zack is called away on yet another mission - this time they are headed to Nibelheim, to investigate reports of monster attacks. [CC]
Cloud comes with Zack and Sephiroth to Nibelheim (suffering from motion sickness in the truck along the way).
Tifa Lockheart is assigned as their tour guide through the Nibel Mountains. She does not recognize Cloud, who is disguised under his military outfit. Someone takes a picture of them before they leave. [FF7 and CC]
NOTE: At this critical juncture, there are several inconsistencies between the original FF7 and CC. CC is essentially a retcon of the FF7 version of events. There are even more inconsistencies if taking FF7: Last Order into account. Last Order is a 30-minute anime included with Advent Children: Collector's Edition, which is not identical with either version. However, it can be assumed that Last Order is not canon, but sort of an intermediate step along the way to Crisis Core. The following are the events as they take place in FF7:
Sephiroth finds the JENOVA and Mako-infused monsters in the reactor, as well as the chamber holding JENOVA itself. He begins to doubt his origins and who he is. He discovers a secret library in Nibelheim where he finds out the truth about himself, that he was created with JENOVA cells from before birth. Overwhelmed by the new information and the lies he was told, he goes on a rampage, beliving himself to be the 'chosen one', the one to rule the Planet, and burns Nibelheim to the ground. Zack and Cloud find that he intends on taking JENOVA, who he now considers his true mother. Tifa runs up to the mountains for revenge, followed by Zack, who is in turn followed by Cloud. [FF7]
As Sephiroth tries to open the chamber to JENOVA, Tifa takes Sephiroth's sword (which he has carelessly left on the ground) and attempts to stab him for the death of her father. Sephiroth gets the better of her and slashes her, leaving her seriously injured on the ground. He enters the inner chamber and takes JENOVA's head from its stasis container. Zack arrives to attack Sephiroth and is also stabbed and lies wounded. Cloud eventually comes, finds Tifa lying bleeding on the ground. Overcome by emotion, he takes Zack's sword, and attacks Sephiroth. Sephiroth easily dispatches him, and runs him through the gut with his masamune. Cloud is seriously injured, but in a haze of emotion, somehow manages to grasp the sword by the blade and reverse the hold, throwing Sephiroth into the Lifestream beneath him. [FF7]

5 - 0 B.G.:

Sephiroth drifts through the Lifestream and ends up in the Northern Crater, frozen. [FF7]
Tifa is rescued by her martial arts instructor, Zangan. She makes her way to Midgar, where she opens a bar in Sector 7 called Seventh Heaven. [FF7]
Zack and Cloud, both barely alive, are captured by Hojo, taken to the basement of the Shinra Mansion (also in Nibelheim), and used as part of his new experiment - to attempt to create Sephiroth clones (clones is something of a misnomer, as he is trying to make another Sephiroth through injection of JENOVA cells and concentrated doses of Mako). Most of Hojo's other victims are from the ruins of Nibelheim. All other the experiments are failures, resulting in a vegetable-like state, and most end up in the slums of Midgar. Cloud does not take to the treatment - the JENOVA cells do not affect him. Hojo labels him a failure, but keeps him around. [FF7 and CC]
Cloud's mind, awash in pain and fear, confused and sick and neck-deep in self-denial, guilt, and shame, begins to construct its own version of the events of Nibelheim. He merges his memories with the role Zack played and takes his position in the occurrences, thinking he became a member of SOLDIER. He also glosses over his friendship with Tifa as if they were best friends. He somehow manages to make his way to the Midgar train station. Tifa finds him there, and decides to watch over him for a while. [FF7 - Why Cloud did what he did is conjecture, but reasonable assumptions can be made]
Shinra orders Nibelheim to be rebuilt and populated with Shinra staff to oversee the actions of the Sephiroth clones from Nibelheim. They are ordered to pretend no catastrophe has ever happened there. (The flashback which shows the escape from Shinra Mansion is only seen in the American and International versions, not the original Japanese version) [FF7]
Hojo takes the remaining body of JENOVA from Nibelheim and ships it to Shinra HQ in Midgar, minus the head that Sephiroth took with him. [FF7]
Hollander, still under attack by Genesis, ends up injecting himself with Genesis's cells (the reasons are still unclear). He begins deteriorating. [CC]

1 B.G.

As above, there are discrepancies between FF7 and CC. The following is the FF7 version:
Zack, still in stasis in the basement of Shinra Manor in Nibelheim, recovers his consciousness. When a guard comes to give Zack his food, he knocks out the guard, rescues Cloud (who can barely move) and escapes. He hitches a truck to Midgar, taking Cloud with him the whole time. After debating with himself, he decides that he and Cloud should become mercenaries. While climbing a cliff overlooking Midgar, they are chased down by Shinra soldiers. Zack is shot dead, but they leave Cloud, who can still barely talk and move. Cloud manages to crawl to Zack's body and take his buster sword.
CC version of events:
Lazard, as the Angeal clone, appears and either breaks Zack out of his cell or wakes him up so he can do so himself. Zack comes to on the floor. He is discovered by Shinra soldiers, but knocks them out, then breaks Cloud out as well. Cloud is suffering from severe Mako poisoning as well as the effects of Hojo's Sephiroth experiments; he can move with assistance, but can't speak. Zack fights off the soldiers he finds and puts Cloud to rest in a bed in Shinra Manor. He finds a SOLDIER 1st Class uniform and dresses Cloud in it (his clothes are soaked with mako). Zack finds the note Aerith wrote him and decides to go back to Midgar to see her.
While Zack and Cloud make their escape, the alarm has gone out that Hojo's subjects have escaped. Shinra sends the Turks to eliminate them, fearful that Zack knows too much. Cissnei finally confronts Zack, unsure if she really wants to go through with it. She attacks him, but Zack fends it off, then runs back to Cloud. Cissnei finally decides to let Zack go, and reports that she lost him. She gives him a Shinra bike (presumably the one she rode). Zack puts Cloud into the sidecar and rumbles off. [CC]
Zack is run off the road by Genesis clones, then encounters the real Genesis. Genesis tears off a piece of Zack's hair - now the only available source of Sephiroth's cells and hence Jenova cells. He feeds it to one of his clones, who mutates into a giant monster. Genesis flies off, leaving Zack to defeat the monster. Zack continues on to Midgar, but on the way he ends up in Gongaga. [CC]
Although Zack had intended to say hello to his parents, Cissnei meets him there. Zack decided to ask Cissnei to talk to them and not put them in more danger by meeting them personally. He also sees Angeal (Lazard), who traveled to Gongaga to try to meet with Zack. However, he is attacked by more Genesis clones, who want more of Sephiroth's cells, and they're led by none other than Genesis and Hollander - deteriorating rapidly and with tiny stumpy wings. Genesis says that Zack's "S cells" aren't pure, since Zack's system rejected them - only Cloud's are. Hollander flies off after Cloud while Genesis keeps Zack busy spouting rubbish from LOVELESS. He finally flies off, leaving him with a dumbapple. [CC]
Zack rushes towards Cloud, to find Angeal/Lazard trying to fight off the Genesis copies. Zack beats them off, and finally gets rid of Hollander. He speaks with Lazard and realizes where Genesis is heading - to the core of the Lifestream, in the ruins of Banora. [CC]
Zack descends to the bowels of Banora and meets with Genesis in a room shining with Lifestream. Genesis uses it to transform into a giant monster, believing this will cure him of his deterioration. Zack finally defeats the monster. Genesis is shown a vision of the "goddess" of the planet - Minerva. What happens next is unclear, but at the end Genesis falls, defeated, but the deterioration is gone. [CC]
Lazard fends off Shinra soldiers with the help of the Angeal copy which Zack saw in the Midgar church. Both Lazard and the Angeal copy pass away from the effort. The next day, Zack decides to do a favor for Genesis, who'd always wanted to share a dumbapple with Angeal and Sephiroth. With Zack standing in for Sephiroth (he has his cells), and Lazard for Angeal, they do indeed share a dumbapple. Both Lazard and the Angeal clone disappear, the latter leaving behind a letter from Aerith, which reveals that four years have passed since Zack's capture, and that she's sent 88 other letters to him through Tseng, none of which came back. [CC]
Weiss and Nero, from Deepground, arrive in a helicopter to take Genesis away with with them. They won't be seen again till DoC. [CC]
Zack and Cloud are pursued both by the Turks (in helicopters) and by what appears to be the entire Shinra army. As Zack nears Midgar, he is confronted by a seemingly neverending battalion of soldiers. His memories slowly fading, Zack falls to the ground, where a soldier shoots him in the head. Cloud, aware that something has changed, manages to crawl his way to Zack's body. Zack, still alive, gives him the Buster Sword and tells him to "live both our lives". Finally, he passes away, and returns to the Lifestream. [CC]