Seemingly an average man, Joe Logan leads a peaceful life in the countryside with his wife and child. However, the Logan family have actually assumed false identities to escape from Joe's past as a fearsome ninja assassin. Despite a string of high-profile murders of his former peers, Joe is sure that his new life is secure—but his tranquil bliss is soon shattered when his family is slaughtered by members of his former clan. Left for dead, Joe wakes up in a hospital, unsure of how he survived the wounds that should have killed him. Police detectives Emma Samanda and Mike Moriss, assigned to investigate the Logan family's deaths, witness another attempt on Joe's life. However, this time Joe is prepared. Unleashing secret techniques, he easily dispatches his enemies, shedding his new identity in the process. Embracing his old ways, Joe shrouds himself in his former persona, cutting through the organization he once served in the name of cold-blooded revenge. Assisted in his hunt by the detective duo, Joe will stop at nothing to kill his past and the demons hailing from it.

The innocent Nagomi Wahira has always admired the cute girls serving at maid cafes. Hoping to fulfill her dream of becoming one, she moves to Akihabara to work at the maid cafe Ton Tokoton. Nagomi's first day seems completely normal—until she has to run an errand at a rival maid cafe along with her fellow recruit, the mature Ranko Mannen. There, things quickly go south, and Nagomi soon gets her first taste of Akihabara's violent maid wars. As she watches Ranko calmly battle her way through a horde of gun- and knife-wielding maids, Nagomi realizes that maid cafes are drastically unlike what she had envisioned. While struggling to reconcile her expectations with the harsh reality she finds herself in, Nagomi searches for the enjoyment she once saw in the lives of maids.

Following a catastrophic war against a race of giants known as the Zentradi, humanity has escaped towards the center of the galaxy aboard a fleet of colonial vessels called the Macross Frontier. As the extraterrestrial threat is left further and further behind, life on Macross Frontier proceeds as usual. In the year 2059, a young mecha pilot trainee named Alto Saotome and his colleagues are preparing to perform an accompanying routine for the famous singer Sheryl Nome, who has come to Macross Frontier for a concert. During the performance, a biomechanical alien species known as the Vajra make a sudden appearance, breaking through the defensive perimeter surrounding the vessel and crash-landing near the concert venue, plunging the entire city into chaos. As the concertgoers evacuate, a young girl named Ranka Lee is left behind and gets targeted by the Vajra, but she is saved at the last minute by Alto. Following these events, the Strategic Military Services program notes Alto's skill in battle, resulting in his recruitment to combat the new alien threat.

The second part of Nanbaka. The prisoners and their guards continue their comfortable lives at Nanba Prison. However, from the shadows emerges a new threat: Enki Gokuu, a person from Samon's past, who has mysterious goals of his own.