Honkai Impact 3rd is set in an alternate version of Earth, plagued by catastrophes resulting from "Honkai" (in Chinese translates as "Chaos", while in Japanese, it is said "Houkai".). Honkai is largely viewed as a malevolent force with a will of its own, able to corrupt humans into undead creatures, manifest itself in the form of various monsters, and select various individuals known as "Herrschers" to imbue with god-like powers able to trigger apocalyptic events. The Honkai is a cyclic phenomenon, returning to end civilization on Earth each time it gets too advanced - the Previous Era ended 50,000 years prior to the game's start, after the 14th Herrscher defeated humanity.
In the present day, various global factions exist to combat or take advantage of the power of Honkai. These include "Schicksal", a European-based peace keeping organization that deploys human warriors known as Valkyries to combat the Honkai; "Anti-Entropy", formerly the North American branch of Schicksal that objected to the use of human soldiers in favor of mechanized robots; and "World Serpent", a shadow organization manipulating events since the end of the Previous Era.
Prior to the story's start, three Herrscher awakenings (or
"Impacts") have occurred in the Current Era: the Herrscher of Reason who
became the leader of Anti-Entropy instead of fighting humanity, the
Herrscher of the Void who was sealed away by Schicksal under mysterious
circumstances, and the Herrscher of Lightning who was prevented from
fully awakening and sent to train her powers as a Valkyrie at
Schicksal's St.Freya school.
The game's story starts with three Valkyries-in-training (Kiana Kaslana, Mei Raiden, and Bronya Zaychik) boarding the Selene, a hostile flying battleship. The three take control of the battleship, then subdue Bronya when she is abruptly controlled malevolently. Following the successful mission, the girls take a graduation exam, during which a mysterious voice contacts Kiana and informs her of her lost parents, Siegfried Kaslana and Cecilia Schariac.
The Valkyries then dispatch to Schicksal's Oceania Branch to recover the Gem of Desire following a local Honkai Eruption that decimated the area. The trio discovers Wendy, who was implanted with the Gem of Desire, and learn that Wendy triggered the Honkai Eruption due to a hatred of Schicksal, which had crippled Wendy. Bronya is controlled again and attacks, causing Wendy to transform into a Herrscher. Although Mei and Kiana are able to subdue both girls, Anti-Entropy forces appear and Bronya kidnaps Wendy and Mei. The Valkyries subsequently track Anti-Entropy to the hijacked ME Corp with Bronya's assistance. There, Bronya destroys the biochip in her brain to free herself from Cocolia's control and enable the Valkyries to escape, but leaving Wendy behind.
Searching for a way to revive Bronya, Theresa Apocalypse creates a
virtual datascape to find data on the biochip. Kiana is transported to a
recreation of Siberia during the year 2000 in the midst of the 2nd
Honkai War. Kiana meets virtual recreations of her parents, Siegfried
and Cecilia, and while Siegfried is badly injured, Kiana and Cecilia
team up and successfully defeat a recreation of 2nd Herrscher, Sirin.
Upon Sirin's defeat, it is revealed that the events that Kiana
experienced were a hallucination created from Kiana's desires by Sirin.
Fu Hua captures Kiana and takes her to Schicksal HQ.
Four months after Sirin's attack, Mei, Theresa, and Bronya
attempt to meet with an intel dealer named Gray Serpent in Arc City who
claims to have seen the Herrscher of the Void, unaware that Otto
Apocalypse had dispatched Rita to obtain his information as well. Rita
seems to kill Gray Serpent and steals his cybernetic implants, leading
the Valkyries to capture a cyborg girl called the Ningyo. Before they
can extract the Ningyo's information, Rita intercepts the Valkyries,
steals the data, and formats the Ningyo's memory. While Einstein and
Tesla attempt to retrieve the Ningyo's lost memories, the team is
contacted by Cocolia, who convinces them to help find the Gem of Desire.
Gray Serpent, seeking payment for the Valkyrie's theft of the Ningyo,
hacks into the Selene. When Bronya follows Gray Serpent into
virtual space, he traps Bronya in a data labyrinth formed from her
memories to deter her. Bronya is able to escape, though she witnesses a
record of the 1st Herrscher, Welt Young, and Einstein battling the World
Serpent, who is sealed within the Sea of Quanta.
After clearing some honkai beasts and being separated, Seele and Bronya reunite and try to escape the labyrinth. The two girls reach the edge of the Quanta but are caught by tentacles. Bronya makes a sacrifice and cuts the tentacles binding Seele, succumbing to the tentacles herself. However, Seele dislikes her powerlessness and the Dark Seele (Velonia) finally agrees to lend her power to Seele, and they use their combined power to rescue Bronya.
Back to Kiana; after recapturing control of her body, she has
been living in exile alone in the Arc City in order not to hurt others
with the Herrscher personality. One night, she is fighting with Honkai
beasts when Sirin seeks the opportunity to torment and brainwash Kiana,
attempting to reawake the Herrscher. Fortunately, Fu Hua reaches Kiana's
mind and drive Sirin away. Kiana holds hatred towards Fu Hua at first,
but Fu Hua tells Kiana that their spirits are combined forever due to
the power of Key of Deity, and that Kiana must learn to control the
Herrscher power by herself. Under Fu Hua's training, Kiana finally
succeeds, and returns to fighting against Honkai in Arc City.