Part I: Ten years after the destructive Great War, the nations of the world decided to turn to espionage rather than open warfare to resolve their conflicts. In the Din Republic, master spy Klaus is given an "Impossible Mission" which if he manages to pull off, will cement his reputation as the "Greatest Spy in the World". As part of this mission, Klaus gathers seven young spy cadets who are struggling in training, including a girl named Lily, into a team codenamed Lamplight. He explains that he will help train them to prepare for an Impossible Mission in the Galgad Empire, but while he proves to be a master spy, he is actually a poor teacher. Thinking that Klaus intends to use them as sacrificial pawns, Lily ambushes Klaus with poison gas in an attempt to force him to disband Lamplight. However, Klaus reveals he already saw through Lily's ambush, but he is impressed how she took the initiative to try and improve her situation, which gives him inspiration on how to teach the other students. The next day, Klaus installs Lily as the team leader for Lamplight and assures them that he won't let any of them die. In order for them to learn the skills they need, Klaus challenges the students to defeat him in a game of espionage.

Part II: For the next five days, Lamplight works together to try and ambush Klaus, but with little success as he easily thwarts their plots. Eventually, the team starts to get frustrated until Lily suggest they actually try investigating Klaus' background. Meanwhile, Klaus is briefed by his superior C that the Galgad Empire stole a sample of a deadly bioweapon from the Din Republic called Abyss Doll, and the Impossible Mission is to retrieve the sample before the Galgad Empire can reverse engineer it. Klaus then returns to Lamplight and comes clean with them, revealing that he is a member of Team Inferno, the Din Republic's best spy team. However, the rest of Inferno was killed trying to retrieve Abyss Doll, and he accepted the mission in order to avenge them. Lamplight, having already learned of his connection to Inferno and inspired by his resolve, agree to follow Klaus. The team then infiltrates the Galgad Empire to collect information on the Endry Lab where Abyss Doll is stored. The night before the mission, Lamplight invite Klaus to attend a party so they call relieve their built up stress. Klaus arrives to find the girls asleep, and he remembers a lesson he was taught where a person willing to sleep in front of another is a sign of ultimate trust. Klaus once again swears to get the entire team home safely. The next night, Lamplight and Klaus prepare to infiltrate Endry to retrieve Abyss Doll.

Part I: Some time after the completion of the Impossible Mission, Klaus returns to the mansion from vacation, where he thwarts more attempts by Lamplight to ambush him. In addition, Grete begins serving tea to him privately in his room and openly flirts with him, leading him to wonder why she has such an interest in him. Klaus is given a second Impossible Mission to hunt down the infamous assassin Corpse, who has killed many politicians and Republic spies. Klaus is also assigned a mission to apprehend an enemy spy, and he takes Lily with him. Though he completes the mission, he is stabbed with a poison needle by Lily, who claims he instructed her to earlier. Klaus then realizes that Grete disguised herself as him and gave false orders to Lily so he wouldn't pick up any hostile intent. While he's impressed with Grete's plan, he reveals he had already caught on to her trap. However, Grete and Lamplight insist on helping him on his missions, which he so far has been handling solo which has been affecting his health. That night, when Grete serves tea to him again, Klaus correctly deduces that Grete has romantic feelings for him. Still impressed with how Grete was able to come up with such an elaborate plan to trap him in such a short amount of time, Klaus decides to have her and Lamplight's strongest members accompany him on the hunt for Corpse.

Part II: Klaus informs Lamplight about the mission to neutralize Corpse. Fearing they won't be picked, Lily and Sibylla attempt a ploy to poison Klaus to prove themselves, but Klaus tricks them into drinking their own poison. Despite this, Klaus picks Lily, Grete, Sibylla, and Sara for the mission and the infiltrate politician Uwe Appel's mansion under the guise of newly hired servants to protect him from Corpse. However, Uwe proves to be paranoid from the assassinations, and is also thrifty and difficult to please, putting strain on the girls. During a break, Grete confides in Sibylla that she is actually the daughter of a prestigious political family, and that she gets physically ill when she has to talk to any men besides Klaus. Frustrated, Sibylla sneaks into Uwe's office to try and find blackmail material on him, but finds that he is actually an ardent supporter of philanthropy and welfare. Uwe catches Sibylla and recognizes her as the orphan who helped bring down a criminal organization. He decides to overlook her trespass, but fires all of the girls. Despite this, Sibylla is still determined to protect Uwe since they have the shared goal helping the country's orphans. She manages to convince Uwe to reverse his decision, and she becomes his personal driver. One night, Corpse makes his move and attempts to shoot Uwe but misses his shot. Klaus, Lily, and Sibylla then chase him into the forest.

Part III: Corpse manages to escape into the forest, leaving the girls with no choice but to keep protecting Uwe until he makes his next move. Head maid Olivia later confronts Grete about refusing to mingle with male guests at a dinner party, and Grete tells a partial lie that she's in love with another man. Later that night, Corpse attacks again, but Uwe is saved thanks to Sibylla's intervention. Olivia then openly becomes suspicious of the girls, warning Uwe how they are acting uncharacteristically calm despite the attempted assassinations. However, Grete points out Olivia's odd behavior as well, and she backs off. Lily, Sibylla, and Sara then secretly confront Grete, suspecting she has been hiding part of the plan from them. Grete admits that she had disguised herself as Corpse and initiated the two previous assassination attempts in order to flush out the real Corpse hiding among the mansion staff. Her cover blown, Olivia attempts to kill the girls with grenades. When Lily suggests they summon Klaus for help, Grete tells her that Klaus will not be coming, so they will have to handle Olivia on their own.

Part I: With the second team still missing, C considers declaring them traitors, but Klaus assures him that he can solve the issue himself. He then explains Lily and her team what the second team had been doing. Shortly after Lily's team left, Klaus designated Thea to lead the second team and issued a test where they would need to touch his hand before the end of the day. However, Monika, Erna, and Annette were notorious in their respective academies for having poor teamwork. Consulting with Klaus, Thea revealed that she wanted to become a spy after being saved once by Klaus' superior, Hearth. Klaus advised that Thea should be more direct with her teammates to get them to work together. She used her ability to discern people's desires to win over Erna and Annette, though she is troubled at how childlike the amnesiac Annette's desires are. Thea attempted to lure Klaus into a trap, only to learn that Monika had already pulled off her own plan, forcing Klaus to shake her hand after she sabotaged all of the mansion's faucets while using the others as a diversion. Klaus decides to take Lily to look for Thea's team while the others take care of his other missions. Meanwhile, Thea's team are relaxing at a swimming pool when Annette is suddenly hugged by a woman claiming to be her mother.

Part II: As Klaus and Lily head out to search for Thea's team, Klaus learns that spies from Lylat and Galgad recently had a covert battle in the city, making the situation dangerous. At the pool, the woman identifies herself as Matilda Barbet, a mechanic from Lylat. While she doesn't intend to hand Annette over, Thea does agree to let Matilda have dinner with Annette in hopes that Annette connecting with her mother will give her a stronger motivation to be a spy. However, during the dinner, Thea and her team notice Matilda is being followed and help her elude her pursuers. Matilda admits that she is being chased by debt collectors because her toolbox was stolen and she was tricked into pawning off her passport in an attempt to get it back. Thea and her team decide to retrieve her toolbox and return it to Matilda. However, Monika reveals that she recovered Matilda's passport but the name on it doesn't match Matilda's, meaning she is a Galgad spy.

Part III: Klaus and Lily arrive in the city, where they notice a covert but heavy military presence and meet their leader, Welter Barth from Military Intelligence. Welter informs them that the military is hunting a Galgad spy loose in the city, and Klaus already suspects the spy has a connection to Annette. Earlier, Thea and Monika come to a disagreement over whether to turn Matilda in to the military or not. Monika gives Thea and Annette one more day to come to a final decision before she reports to Klaus. Thea and Annette meet Matilda again, and she admits that she became a spy in order to support to Annette, and promises to retire if she can escape the Republic with her. Thea recalls the time she was saved by Hearth and how she wanted to become a hero like her, and both she and Annette decide to save Matilda. Thea and Monika then have a confrontation, and Thea is able to figure out that Monika is secretly in love with somebody in Lamplight. An embarrassed Monika agrees to go with Thea's plan to keep her secret, but warns that somebody will eventually take advantage of Lamplight's kindness. The next day, Thea assures Matilda that they will help her escape the country if she promises to retire as a spy. However, it appears that Matilda is actually manipulating Thea and her team.

Part I: White Spider meets with fellow Serpent member Purple Ant in the city of Mitouza in the United States. White Spider explains that the Tolfa Economic Conference will begin soon, which will attract spies from all over the world, and orders Purple Ant to eliminate them all, including Klaus. Meanwhile, Klaus assigns Thea to lead the mission, but she remains self conscious about her failures to deal with Corpse and Matilda. After Klaus and Thea visit Corpse at a secret prison, Klaus realizes that Annette has sabotaged their car in an effort to get him to admit defeat. Klaus if forced to ditch the car where he is ambushed by Lamplight, but he is narrowly able to win due to calling the police ahead of time, forcing Lamplight to flee. However, Klaus is impressed with their growth and tells them their next mission will also double as their graduation exam. Realizing Lamplight was able to pull off such an ambitious plan without her involvement, Thea grows even more self conscious. Klaus and Lamplight then arrive in the United States and quickly infiltrate various areas of Mitouza to gather intelligence, though they also learn that foreign spies are being killed. It is also revealed that they had brought Corpse with them as their prisoner in order to identify Serpent.

Part II: Lamplight continues their intelligence gathering, though Klaus warns that numerous foreign spies have been killed so far. Grete's main worry is that since Lamplight's training is focused on attacking Klaus, they have a lot of experience being on the offensive but little training to defend themselves against enemy spies. During the night, a politician's chauffeur named Barron attempts to drug Sibylla, but she thwarts the attempt and chases Barron into an abandoned building, which turns out to be a trap. Fortunately, Erna arrives to assist Sibylla against Barron. Meanwhile, Lily is framed for a murder and the police attempt to arrest her, and she is rescued by the intervention of Annette. Monika is lured into a high stakes game of darts by a woman named Miranda, and is narrowly able to defeat her by deflecting her dart. However, instead of giving any information, Miranda stabs herself in the neck with a dart. In a flashback, Purple Ant boasts to a wounded spy that he has filled Mitario with his "Worker Ants", regular citizens who he has brainwashed into his own army of sleeper agents.

Part III: Monika manages to thwart Miranda's suicide attempt by knocking her unconscious. Meanwhile, Sibylla and Erna are able to defeat Barron, but upon learning that Barron was coerced by Purple Ant under threats to his family, Sibylla prevents him from letting himself bleed to death. However, despite their successes, Lamplight are ambushed by additional assassins. In the flashback, Purple Ant boasts to Hearth that he has hundreds of expendable Worker Ants in Mitario that he can use to overwhelm enemy spies, and then shoots her in the femoral artery. In the present, Grete heads out to support the others, leaving Thea to wonder how she can help in the situation. Annette then informs Thea of a rumor of a black haired woman assuring the Worker Ants a hero will save them, and Lily suggests Thea take advantage of that. Thea then confronts Corpse, who offers to help her since unlike the other Worker Ants, he didn't commit suicide. Thea frees Corpse, who immediately attacks and captures her before turning her over to Purple Ant.