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In the year 2029, the barriers of our world have been broken down by the net and by cybernetics, but this brings new vulnerability to humans in the form of brain-hacking. When a highly-wanted hacker known as 'The Puppetmaster' begins involving them in politics, Section 9, a group of cybernetically enhanced cops, are called in to investigate and stop the Puppetmaster.

Two years have passed since the final battle with Sephiroth. Though Midgar, city of mako, city of prosperity, has been reduced to ruins, its people slowly but steadily walk the road to reconstruction. However, a mysterious illness called Geostigma torments them. With no cure in sight, it brings death to the afflicted, one after another, robbing the people of their fledgling hope.

In Japan, the vampire-hunter Saya, who is a powerful original, is sent by her liaison with the government, David, posed as a teenage student to the Yokota High School on the eve of Halloween to hunt down vampires. Saya asks David to give a new katana to her. Soon she saves the school nurse Makiho Amano from two vampires disguised of classmates and Makiho witnesses her fight against the powerful demon.

The interplanetary spacecraft Galileo II carries Atom and his friends to Titan, a satellite of Saturn. However, what awaits them when they arrive there is an attack from an unknown entity. What appears is a mechanical life form called "Igza" that wants to destroy humans. The battle between Atom and Igza unfolds in the far reaches of space.

A member of an elite paramilitary counter-terrorism unit becomes traumatized after witnessing the suicide bombing of a young girl and is forced to undergo retraining. However, unbeknownst to him, he becomes a key player in a dispute between rival police divisions, as he finds himself increasingly involved with the sister of the girl he saw die.