"Hamamura Nagisa no Keisan Nooto" (Hamamura Nagisa's Calculation Notes) volume 2 by Aoyagi Aito. A continuation on the story where many passionate mathematicians took the career path of terrorists. The focus is still math, although volume 2 has more of an amusement park feel to it.
The amusement park aspect arises from how the chapters were organized: while discovering the underlying math principles were key to solving the cases for volume 1, for volume 2, the basic concepts are described early on in each chapter, and the rest of the chapter build on these concepts. Results include a Rubik's Cube themed villain, in a Rubik's Cube mansion filled with Rubik's Cube related traps, killing people in duels using Rubik's Cubes. It was really over the top.
The most over the top bit was the parody on "Alice in Wonderland". It's not the first parody of the classic novel, and it definitely could have expanded a lot more beyond a single chapter, but it's probably the best treatment of positional notion and base conversion that I have seen. Also, in similar spirit to the best mystery stories, there were enough hints in the chapter for readers to work out all the riddles before the end of the chapter. I wish math textbooks would include stories of this sort.
While the math bits continue to be great, on the background plot of terrorism, the number of villains have only increased. There is minor progress in finding Dr. Pythagoras, but I am sure the author is in no rush to resolve those bits, so long as there are more math topics to write about.
Previous (2014-12-18): "Hamamura Nagisa no Keisan Nooto" by Aoyagi Aito
Next (2015-01-14): "Alice's Adventures in Wonderland" and "Through the Looking-Glass" by Lewis Carroll, illustrated by Kriss Sison