Spy Kyoushitsu's first season recieved mediocre critics at best. It did many mistakes - messing up everywhere from a too fast pace to seemingly screening the episodes in the wrong order. It's mystery wasn't thrilling and the cast was far too big to give proper development to the individuals. So it's hardly a suprise the expectations for the second season weren't exactly high. The story of this season just continues where Season 1 left off. With Grete, Lilly, Sara and Sibylla getting the spotlight in the last arc of Season 1, Season 2 starts with a story around Anette, Thea, Monika and Erna. After theysuccessfully completed their mission, they take a few days off, but their vacation is cut short by a fateful encounter. This encounter forces the girls to make some very difficult decisions, and shows them the true reality of their life as a spy. All without their teacher giving advise and protecting them from harm.
This arc does a great job in giving Anette, Thea and especially Monika some much needed development and growth. And at the same time, it tells a great and exciting story with a lot of twists, mystery and action. Something both Arcs of the first season didn't manage to do.

After the first excitement follow three filler episodes, just like in season 1. They focus on Monika, Thea and Anette and work well to satisfy the interest gained in the characters from the previous arc. Monika gets mostly backstory, Thea's story focuses on her values and inner conflict and Anette's goes deeper into explaining the "method in her madness". They also manage to hit with the comedy where Season 1's fillers missed.

The final arc rounds up the first "act" of Spy Classroom, connecting the dots of the first 3 stories told. It does a great job of highlighting each of the girls and how much they've grown, both individually and as a team. But the main focus is on Thea, Klaus and their backstory with the previous members of Lamplight.
This arc once again suffered from slightly high pacing, but unlike the first season's arcs, it's no problem to follow the plot and enjoy it. And it did a great job in finishing the season(s).

Last episode is Lilly's filler - a funny comedy episode. But that's only half of it, as the other half is about Thea processing the previous arc. It finishes with a nice bridge between the two halfs anf finally a tease of what would be next in a potential 3rd Season.

In conclusion: The second season of Spy Classroom is nothing like the first. It fixes all the major problems and finally makes use of the great potential this show's characters and world-building have.

If you cared about the first season enough to look up reviews for the second - go watch it. Even if you are disappointed and conflicted on whether to continue. It was the same for me. If you've come this far, keep going!