“The Situation Beneath the Surface” “Suimenka no Jōkei” (水面下の状景)

Sousuke and Kazama investigate who is posting embarrassing and revealing pictures of Kaname on the internet. Meanwhile, Amalgam operatives led by Gates extract payment from the Balic military force that took on Mithril and try to reconstruct what happened in the battle.

“Ending Day by Day” “Owaru Hibi” (終わる日々)

Mithril and the SRT rescue refugees caught in a civil war in the African country of Balic. However, during the fighting, they discover that the enemy possesses advanced weaponry rivaling their own. They surmise that a highly funded, well-equipped organization may be supplying their enemies.

通り雨にて 或いは、少女はいかにしてその心情に至ったか? Tōriame ni te arui wa, shōjo wa ikani shi te sono shinjō ni itatta ka? In the Passing Rain, Or, How Can a Girl Have Reached Such Feelings? ~ Regenschauer (lit. Heavy Rain)

“Evanescent Encounter (Part 3)” “Circle of Transmigration 3 / Shōji Ruten sono san” (生死流転 其之参)

As Fuu finally confronts the Sunflower Samurai, Mugen and Jin face their ultimate tests. While Mugen must face the remaining brothers, Jin continues his battle with Kagetoki Kariya. And there’s the small matter of their own duel.

“Evanescent Encounter (Part 2)” “Circle of Transmigration 2 / Shōji Ruten sono ni” (生死流転 其之弐)

As Jin duels Kagetoki Kariya, the most powerful man in the shogunate, Mugen has to contend with three brothers who want his head. Will they survive?

“Evanescent Encounter (Part 1)” “Circle of Transmigration 1 / Shōji Ruten sono ichi” (生死流転 其之壱)

Fuu, Mugen and Jin have finally arrived in Nagasaki to find Ikitsuki island in search of the Sunflower Samurai. There seems to be one small problem that might keep them from getting there though. A group of assassins are following closely behind.

“Baseball Blues” “Heart and Soul Into the Ball / Ikkyū Nyūkon” (一球入魂)

An American sea vessel arrives in town and a canny ninja-turned-team manager enlists our heroes to do battle with them on the field of honor…which in this case is a baseball diamond. Behold Mugen’s pitching skills and tremble!

“Cosmic Collisions” “Anger Shot Toward Heaven / Dohatsu Shōten” (怒髪衝天)

On the way to Nagasaki the trio fall through a mine shaft. They’re introduced to its charismatic owner and start working for a share of treasure. As the days drag on the things take a turn for the bizarre.

“Elegy of Entrapment (Verse 2)” “Generous Elegy 2 / Hikakōgai sono ni” (悲歌慷慨 其之弐)

Jin learns the Way of Water, a woman’s sorrow comes to an end, and Mugen both gives and receives an assassin’s last gift.

“Elegy of Entrapment (Verse 1)” “Generous Elegy 1 / Hikakōgai sono ichi” (悲歌慷慨 其之壱)

Fuu, Mugen and Jin meet up with a blind girl who is a traveling musician. Because of her blindness, she is able to sense the emotions of the group. Is this girl more than just a musician?

“Unholy Union” “Karma and Retribution / Ingaōhō” (因果応報)

A cynical charlatan fleeces the hidden Christian flock, Fuu gets closer to the Sunflower Samurai, and a truth is finally revealed.

“War of the Words” “Pen in One Hand, Sword in the Other / Bunburyōdō” (文武両道)

Fuu gets a facelift when kids trade in the sword for the graffiti brush; Jin keeps a promise to a long-lost friend and confronts the shock of the new, while Mugen learns to read and conquers a castle.

不還 Fugen No Return ~ Erleuchtung (lit. Illumination)

Mariko regains the ability to use her vectors and stages one final meeting with Lucy. They meet, and Lucy goes into a state of shock after losing one of her horns. Kurama, accompanied by Nana whom he rescued after she fell off the bridge where she battled Mariko, encounters their fight. Here, Mariko realizes that Kurama is her father and meets him for the first time, beginning to cry after finally encountering her father, who appears to have abandoned her for Nana. Kurama exchanges final words of reassurance to Mariko just before the final bomb inside her is detonated, killing them both. The Director of the facility that had been holding Lucy, Nana and Mariko reveals that he is a diclonius. Lucy, who makes it out of the fight alive, reveals her remorse and emotion for Kohta and they kiss before she leaves to encounter the security team. However, Lucy’s ultimate fate is unknown except that her other horn is broken, although it is possible that she died as the shots of the guns continue, even after her horn is broken. The “family” of Kaede house, including Nana, settles down. As they are about to eat, Wanta barks at someone at the door. When Kohta goes to check, the music box playing “Lilium” stops and he sees a figure standing at the front door. He then hears the grandfather clock, which Lucy had repeatedly attempted to repair, ticking again.

泥濘 Deinei Quagmire ~ Taumeln (lit. Tumble)

The past which Kohta had tried to forget eight years ago comes back to him as he remembers that Lucy took revenge on Kohta’s lie about the gender of his cousin by killing Kohta’s father and his sister Kanae. As Shirakawa dispatches Mariko to kill Lucy, Bando is paid by Kurama to kill her as well. Mariko is about to kill Nana (as well as Kohta and Lucy), until Nana uses her vectors to deactivate Mariko’s and falls off the bridge, as Mariko’s vectors fail and she is taken away. Shirakawa discovers Lucy’s Nyu personality and identifies her as the target diclonius, only to be killed along with the security forces enlisted to guard against Mariko.

錯綜 Sakusō Complication ~ Vermischung (lit. Intermixing)

Mariko is revealed to be the true identity of No. 35. Under supervision from staff at the facility, she is released as a last effort to retrieve Lucy. Nana senses Mariko’s presence and her desire to kill her through their ability to locate each other. Mariko and Nana meet on a bridge on the shore and they battle. Kurama, who supposedly “had to leave”, has joined Bando to kill Lucy on his own beyond the knowledge of Shirakawa and the staff.

嬰児 Eiji Infant ~ Säugling (lit. Infant)

Kurama’s past is explained in this episode. He was a good friend of Professor Kazukawa, who invited Kurama to work with him and his father on the diclonius project after leaving university. He reluctantly agrees, however, as he is performing research, he is infected with the diclonius virus via transmission through their vectors, and as a result, his daughter Mariko is born a diclonius. He decides to kill her, however as his wife dies from complications after giving birth, begging him to spare her, Kurama chooses to let her live under Kazukawa’s condition that bombs must be planted inside her to kill her in case she turns aggressive. Meanwhile, as both Lucy and Nana are now part of Kohta’s household, the facility decides to send “the most powerful” diclonius, known only as “No. 35”.

“Lullabies of the Lost (Verse 2)” “Idling One’s Life Away, second verse / Suiseimushi futa yume” (酔生夢死 ふた夢)

Jin ends a life he hoped to spare. Continuation of the last episode.

追憶 Tsuioku Reminiscence ~ Schöne Erinnerung (lit. Beautiful Memory)

Lucy’s past links with Kohta are uncovered - after her dog was killed, she began to show contempt for humans, until Kohta briefly befriended her. Kohta plays the series’ opening theme “Lilium” in a music box which he bought in Kamakura. They go to the zoo and later play in the water, where she thanks Kohta for the most fun she’d ever had in her life. Her hope in being re-acquainted with humans is briefly regained. However, when she discovers Kohta’s cousin (Yuka), who he claimed to be a boy, is actually a girl, she loses hope and begins her future murderous path.

“Lullabies of the Lost (Verse 1)” “Idling One’s Life Away, first verse / Suiseimushi hito yume” (酔生夢死 ひと夢)

Mugen, Jin and Fuu get into a quarrel and separate, and have unexpected encounters; new opponents appear, old grievances return, and Mugen and Fuu meet a mysterious archer.

嚆矢 Kōshi The Beginning ~ Beginn (lit. Beginning)

As a result of living her entire life inside the facility, Nana is found to be naive and sensitive about the events surrounding her. Mayu discovers the real Lucy behind Nyu as Nana tells her of their diclonius powers. As Lucy is recovering from being hit in the face by Nana, she goes through a flashback of her childhood, where she was raised in an orphanage all her life where her peers constantly bullied her. Feeling lonely and ignored, she begins to develop her hatred for humans. When her peers discover that she has made friends with a stray dog, (discovered when a girl pretended to be Lucy’s friend) they force her to watch as they beat it to death with a vase, and in her despair, Lucy activates her vectors and commits her first murders against her schoolmates.