The overarching plot of Seton Academy: Join the Pack! is less a continuous narrative and more a series of episodic adventures tied together by the growth of the Cooking Club. The central spoiler is the true nature of Jin Mazama's feelings. While he publicly maintains his hatred of animals and his crush on Hitomi, it becomes increasingly clear that he has developed deep protective feelings for Ranka and the rest of the pack. This is a classic 'tsundere' arc, where his actions betray his harsh words; he repeatedly saves the day using his knowledge and quick thinking.
A significant mid-series twist involves the arrival of Team EX, a group from a rival academy composed of students from 'extinct' species like a Neanderthal (Anne), a Barbary lion, and a Woolly Mammoth (the leader, Man). Their goal is to take revenge on modern species and humans, whom they blame for their extinction. Anne Anetani initially tries to infiltrate and break up the Cooking Club but is eventually won over after learning that modern humans share Neanderthal DNA, leading her to make peace with the group and develop a crush on Hitomi.
The series finale culminates in a school-wide competition that pits the Cooking Club against Team EX, settling their differences through a one-on-one boxing match between Ranka and the Woolly Mammoth. Ranka, using a strategy devised by Jin, manages to win through sheer tenacity and surprise, not by overpowering her opponent. The victory solidifies the Cooking Club's status and reinforces the show's theme of cooperation triumphing over conflict. In the final moments, just as peace seems restored, the student council president King Shishino appears, heavily beaten, warning of an invasion from an Insect Academy, serving as a cliffhanger that teases future conflicts from the manga.