LOOSE STORY. QUESTIONS GO IN COMMENTS. UNNECESSARY SENTANCE.
Immediately after the events of X8: Axl is rushed to the emergency Hunter care center. The doctor looks away for a second (don't know why) Only to turn back seeing Axl running away.Axl becomes a bad guy, but with the attitude of Sigma(?) (because at the end of X8, he got infected with a highly volotile form of Sigma Virus) Neo Green (AKA GBD) Is a third character. He chooses to help because the Maverick Hunters gave him a second chance. During all of this, humans realize most of their wars have been caused by reploids. A small group of Humans (4000-5000 people) Start killing reploids, at an increasingly fast rate. Realising his Great-Great-Great Grandfather's work is being destroyed, John Light combines all of Thomas's work into one entity, known as the Mother Elf. John Light then delivers the Mother Elf to the Hunters, knowing they will benefit greatly from having it. 9 mavericks (one optional) appear out of nowhere, claiming to be the followers of their fallen leader, Sigma. [FINAL BATTLE TIME] . Three forms: ONE – Axl as himself; he’ll switch between attacking you as himself and using the DNA he’s accumulated to do different attacks. TWO – Axl becomes supercharged with the Sigma Virus, being able to do powerful attacks. THREE – Axl is completely engulfed by the Virus, any of his personality is now gone, replaced with Sigma’s entity. Axl (well Sigma at this point) makes his last transformation to turn into the usual giant boss at the end of every Mega Man X game. X/Zero use the Mother Elf to wipe out the virus contained within Axl. This would close the X series and start the period known as the Elf Wars, which is followed by the Zero series.