Zouken is a major antagonist on the Heaven's Feel route. He presents himself as the grandfather of Shinji and Sakura but it was later revealed that he was present during the founding of the Fuyuki City Holy Grail War 200 years ago back when his family name was Makiri. Zouken is stern, cold, and absolutely single-minded and ruthless in his pursuit of his goal of ultimate power.
Zouken had been alive for about 500 years. Around 200 years ago, the Tohsaka family, Makiri family, and Einzbern family worked together to initiate the Fuyuki Holy Grail War. Zouken was present along with Justeaze von Einzbern and Kischur Zelretch Schweinorg. The Makiri specializes in binding magical familiars to a magus' command and is responsible for creating the Command Spells.
Zouken wishes to use the Holy Grail to gain access to the point of the origin of everything, and to gain immense knowledge and power. He was also in love with Justeaze von Einzbern. Justeaze sacrificed herself to become the base structure of the vessel of the Holy Grail. Zouken was greatly saddened by her sacrifice and swore to see the success of the Holy Grail War. He kept himself alive for the years to come in order to do so.
During the following years, Zouken experienced increasing difficulty in maintaining his existence, thus he became obsessed with trying to continue to exist.
The Matou family was losing its magical powers in its recent years. The latest in line, Shinji was completely incapable of magic. Zouken requested to adopt Sakura from the Tohsaka family, because Rin was already chosen as the successor of her family being the older sister, and that he did not want the Matou magus family to die out.
Sakura was adopted into the Matou family 1 year before the fourth Holy Grail War, 11 years before the fifth Holy Grail War. Zouken subjected Sakura intense training which caused her to suffer greatly and became emotionally withdrawn.
The fourth Holy Grail War concluded with the Holy Grail being shattered by Kiritsugu's Servant Saber. Zouken knew about the Servant Avenger, Angra Mainyu who was laying dormant within the Holy Grail. He implanted a piece of the Holy Grail and his worm familiars into Sakura in order to turn her into an artificial Holy Grail. He bound Avenger to Sakura as her Servant and planned to feed her with the defeated Heroic Spirits of the next Holy Grail War in order to bring Avenger into the world.
During this time, Zouken kept his plan secret from Shinji in order to prevent him from discovering Sakura as the real successor of the family and to prevent him from compromising his plan. Shinji managed to find out and was devastated. He dared not defy Zouken's wishes but he abused Sakura for stealing his right as the successor.
When the fifth Holy Grail War started, Sakura managed to summon Rider. She did not want to fight, so Shinji convinced Zouken to allow him to fight in her stead in order to prove himself as the rightful successor of the family.
Zouken wasn't seen on the Fate and Unlimited Blade Works routes.
Zouken was first seen outside the Matou house. He warned Shirou to not get involved with the Matou family. Later, Zouken witnessed Shinji and Rider losing to Shirou and Saber and voiced his disappointment in Shinji. He decided to take a more active role in the war.
Zouken noticed that the Servant Avenger, Angra Mainyu, in the form of Sakura's shadow, was becoming active as well. He allied with it and summoned True Assassin, who took over Assassin's shell. Avenger also devoured Caster and regurgitated it for Zouken to use against Rin, Archer, Shirou, and Saber. Saber struck down Caster and Archer struck down Zouken. Avenger then attacked them, allowing Zouken to retreat. Zouken devoured a woman to recover. He met True Assassin soon after that and form a contract with him.
The following day, Zouken and True Assassin met Shirou and Saber at Ryudou Temple. Saber was devoured by the black shadow then True Assassin attacked Shirou. Rider then appeared to save Shirou.
Later, Zouken, True Assassin, Saber, and the black shadow assaulted Einzbern castle to devour Berserker. Zouken invited Shirou to explain his plan and that Sakura and Avenger started to act outside his control.
Later still, Shirou and Kotomine went to Einzbern castle to rescue Illyasviel. Kotomine used his exorcism to deal a fatal blow to Zouken. He managed to survive because several of his worms were within Sakura.
On the last day of the war, Zouken and Sakura were watching the opening of the Great Holy Grail. Sakura then decided to betray Zouken by purging herself of Zouken's last worm parasites from herself.
In the true ending, Zouken still hasn't died and was desperate to survive. Illyasviel then appeared and he sees Justeaze in her as Illyasviel is designed after Justeaze. Zouken then remembered his original purpose for staying alive for so long and realized he had failed to achieve it. He then accepted his end.
Zouken uses worm familiars and his body is made up of his worm familiars. The worm familiars are used to devour people for sustenance. As long as a single worm is still alive, Zouken cannot be killed.
Zouken implanted several worms in Sakura to turn her into a Holy Grail. The worms feeds off her magical energy to maintain her as a Holy Grail. Zouken planned to command the worms to devour Sakura and take over her body once the Servant Avenger, Angra Mainyu to take command over Avenger.