The story has many characters. To help keep them straight I have put them in a list for reference and organized them by groups.

****Spoilers!!!****

Qin Royalty Family - The monarchs of Qin, supposedly descended from the ancient Wise Tyrant

King Shorlin - King of Qin, father to King Aou and [redacted], ruled into his old age

King Aou - King of Qin, son of Shorlin, Grandfather to Zelda, known as the Betrayer King, ruled into his old age

King Xiang - King of Qin, son of King Aou, father to Prince Kyou and Princess Zelda, ruled for 4 years

Prince Kyou - son of Xiang and half-brother to Zelda, betrothed to Reida, raised by Chancellor Ketsu

Heir Apparent Zelda - Heir apparent of Qin, Daughter of Bi Ki and King Xiang, half-sister to Prince Kyou, known as Ice Witch

Prince [Redacted] - son of [redacted], uncle of [redacted]

Mitagi clan - The firstborn of the ancient hero, they are known for their skill, might, and honor in war.

General Mouson Mitagi - Lord of the Mitagi main branch

Mouhon Mitagi - Heir to the Mitagi main branch, son of Mouson, rival to Link and Mouki

General Ouki Mitagi - Legendary general, married Kyou Mitagi and joined the Mitagi side branch, rival to Harken Dragmire, known as the Great Bird of Qin

General Kyou Mitagi - General of the Mitagi, married Ouki Mitagi, he was murdered by Harken Dragmire, son of [redacted]

General Geoffrey Mitagi - Originally a crusader, enslaved by Arabs in the crusades, sold to Gerudo, then gained freedom through Ouki, now serves him as his second

Rebellious Hero - [Redacted], also known as [redacted]

Ki Clan - The secondborn of the ancient hero, they are known for their cunning and scrupulous nature.

Bi Ki - Favored concubine of King Xiang, Mother to Zelda, Queen Mother responsible for Royal Harem

Kei Ki - brother to Bi Ki, One of the lords of the Ki underground, uncle to Zelda, known as The Beheader

Satakarta - One of the lords of the Ki underground, Chancellor Ketsu's second, formerly known as [redacted], sold his soul to [redacted]

Sheikah Clan - The secret thirdborn of the ancient hero, known for their extreme loyalty and espionage acting as spies and assassins.

Impa - Shadowmaster of the Sheikah, minister, and Chancellor of Qin, loves Zelda like a daughter

Zant - Elite Sheikah, loyal to the throne, part of an experiment conducted by the [redacted]

Solitare - Elite Sheikah, has a crush on Link, part of an experiment conducted by the [redacted], named Kyou Kai

Fae - Beings with power over nature, firstborn of Farore, are hunted by a slave trade started by The Betrayer King and [redacted]

Tetsu - Fae charged with serving Zelda 

Elder - Lord of the Qin Fae Groves

Ketsu Family - Nobles in service to the Qin Royal Family

Chancellor Ketsu - Chancellor of Qin, favored by King Aou, tutored Prince Kyou, lord of Jouket and its surrounding regions

Shi Ketsu - Serves Zelda as her head minister

Dragmire Clan - Descendants of the ancient Demon King, almost extinct after The Betrayer King was done with them.

Harken Dragmire - Lord of the Dragmire, rival to Ouki Mitagi, sold his soul to [redacted]

Malon Dragmire - Daughter of Kuroko, ward of Ganondorf, likes animals and hunting

Ganondorf Dragmire - Grand Executioner, champion, and Chief of the Majora, bearer of the Mark of Power, adopted son to the twin witches

Kuroko Dragmire - Formerly a slave but gained freedom through the Ki family, mother to Malon

Majora - Mountain tribe west of Qin, known for wolf companions and magic masks, descended from ancient Hyrulian monster hunters

Nabooru - Ganondorf's beta, leader of the hunting parties

Twin witches - Priestesses of Din, mothers to Ganondorf

Link's Unit - An independent warband led by Link

Link - The leader of the unit

Kyou Kai - Link's second off and on the battlefield, known as Solitare

Tou Bi - An old friend of Link's, like an older brother

Hei Bi - known as Bucktooth, an old friend's of Links, like a brother

Den Yuu - Officer of Link's heavy-hitting squad

Kyo Gai - Primary officer of Link's infantry and training

Animals - 

Kagami - Ganondorf's wolf companion

Andim - Zelda's hawk, named in honor of Midna

Ryo's Faction - A political group with most of the power in Qin seeking to take the throne

Chancellor Ryo Fui - A merchant who worked his way to the top of Qin, rival to Zelda, friend to King Xiang

Abhdan - ambassador and former chancellor, teacher to both Zelda and Ryo

General Moubu - man of war, father of Mouki

Mouki - son of Moubu, rival to Link and Mouhon

Shou Hei Kun - Man of strategy, Qin's primary strategist

Ri Shi - Man of law

Other military of Qin - In times of war there are generals and leaders outside of the primary factions and clans

General/Duke Hyou - Known as Duke Hyou or The Duke, has a drink that is considered lethal by most, known for his red hair, sharp teeth, and loud personality. neutral to politics

General Mou Gou - An old general, neutral to politics, father of Moubu, grandfather of Mouki

Commander Matsubi - Leads the former royal guard warband, loyal to Zelda

Commander Kagumi - formerly the commander of the royal guard, teacher to Matsubi

Other members of Qin - People who don't fit in any above clan, family, faction.

Sarah - Zelda's favored concubine, serves in the Royal Harem

Midna - Orphan girl, Link's best friend and adopted sister, could pass as [redacted] look-alike or twin

Twilight - A smuggler in Zhao and hidden agent of Ryo's

Midnight - A smuggler in Zhao

Dawn - A smuggler in Zhao 

Mayor of Jouto - Runs a plantation in western Qin, took in Link and Midna as slaves

Tuoniao - Eunice in the Royal Harem, Sarah's handler

Ghiradrim - known as the wish-granter, a governor of Qin

Lu Buwei - Known as The Kingslayer, a mysterious and powerful man who killed the Zhao dynasty and replaced it with Toujou. Disappeared immediately after but is rumored to be hiding in Qin.

Zora - An aquatic race in eastern Hyrule, secondborn of Farore

Siren Ruto - A Princess of Zora

Lenovalarinalbacrin - A Zora doctor

Zhao - Country north-east of Qin with deep-seeded hatred for Qin

Riboku - Mysterious man of Zhao

King Toujou - King of Zhao, Held Qin royal family hostage briefly, not nice guy, pretty much a sicko