Heres my personal take on the story
The story starts with the siblings Jin, Ragna and Saya a few years before the Ikaruga Civil War(more on that later). One day they are visited by Terumi(aka Hazuma) and either one of two things happened, either Terumi manipulated Jin or transformed into him. Either way Ragna lost his arm and Saya was killed(supposedly). Sometime afterward Ragna was saved by Rachel and Jubei and became a vampire in the process and gaining a new left arm that contained the Azure Grimoire, he was then trained by the legendary warrior Jubei for an uncertain amount of years while Jin was adopted by the Kisaragi family and obtained the Nox Nyctores Yukianesa which amplified his insanity to the point we see in the game.
Around this point in time the Ikaruga Civil War also took place, which Jin participated in and gained his current rank. The Ikaruga Civil War(also called the Second Magic War) was started over the fact that the library had monopoly on the Grimiores, the all important texts necessary for magic use. This created a gap between those who could and could not use magic which resulted in the formation of the Ikaruga Federation who opposed the library and paid dearly for it. Ikaruga was wiped out and the Library now had a complete dictatorship over the world thanks to the Grimoires and killed anyone who opposed them. A few years after this though Ragna began destroying Library facilities which housed clones of his dead sister Saya. After destroying two facilities single-handedly he made his way to the 13th hierarchical city of Kagutsuchi.
On he fought his way into the Library facility he encountered yet another clone of saya named V-13. Unfortunately though Ragna can not unleash his true power against someone who looks so much like saya and is thrown into the abyss along with v-13 who contains the other half of the Azure Grimoire and they create the Black Beast. It is at that point it is revealed that this is at least the 30th time this has happened and that the world of Blazblue is stuck in a 100 year time loop. Only three people are aware of this time loop, Rachel Kokonoe and Terumi, though they cannot do anything to directly stop the loop they can change small events in hopes of creating a difference. The biggest variable that is created is Hakumen. When Jin jumped into the abyss after Ragna and V-13 he is saved by Rachel and sent back in time as Hakumen where he lead the other 5 great warriors to seal away the Black Beast. After the Black Beast was sealed away Hakumen was sent into the "Zone" where he lay waiting until Kokonoe brought him out in the current time period. It is at this point that we enter the True Ending Scenario.
In the True Ending scenario two big variables are introduced into the equation. The first being Hakumen while the second is Noel but more on that in a bit. Everything proceeds as normal until Ragna reaches the center of the library and it is at this point that he is confronted by Hakumen. At this point he is forced to unlease the Azure Grimoire to defeat him which later also allows him to defeat V-13. Though he defeats V-13 he still almost falls into the abyss again though is saved by Noel at the last minute and it is at this point revealed that Noel is also a Saya clone named U-13 and obtains the true Azure grimoire, with Ragna and V-13s being two half's of a fake copy. While this is happening Rachel activates the Tsukuyomi shield to protect the planet from Takemikazuhi(this is the same cannon shown in the opening but ast to who built it or for what ourpose is unknown). Meanwhile back in the Library Hazama reveals himself to be Terumi an unknown villain with unknown objectives who posses incredible power. Though all he does is make the typical bad guy threats and takes his leave. Somehow though he manages to retain his identity as Hazama and assigns Jin and Noels schoolmate Tsubaki to kill the two of them.
Also keep in mind that the entire story mode is one big chess game between Rachel and Hazama since they are the only one aware that time is looping but at the same time are unable to have any direct affect fro some reason. That is why rachel does not take any action to stop Takemikazuchi until the true ending since it is the only time line where Ragna beats Nu-13. Though unfortunately this allows Hazama to manipulate Noel a bit but as to how well just have to wait till the next game.