In the second season the story continues exactly where it left off previously. Professor Itsuki's Fermentation Cellar and laboratory is ready for operation and with Sawaki Tadayasu's unique gift to see and communicate with microbes to help, Itsuki's motley group of students begin to process different fermented products like soy sauce and sake. (Source: ANN)

Lupin & co. attempt to steal two face plates from millionare Michael Sizuki, thinking that they will lead to an ancient treasure when brought together. However, it soon becomes apparent that there is more behind the plates then meets the eye. 

(Source: ANN)

Two jewels are the key to the ancient treasure of Yaobikuni. But legend has it that the only person who can find the treasure is one who can walk the path of death.

And why is Lupin interested? This is the one treasure his grandfather sought but did not steal.

(Source: AniDB)

The tests have come, and Keitaro can only hope to succeed. However, in the final stretch, he fails miserably and daydreams through the test. Assuming that he has failed, he runs away, so the rest of the cast hunts him down on a remote desert island to bring him back. The Toudai entrance exams have finally come (again) for Keitaro. With all his confidence Keitaro sits for the paper, but ends up falling asleep and dreaming about Narusegawa. Waking up with barely any time to complete the paper, Keitaro thinks he will fail the paper and tries to escape from Hinata Lodge and forget all the memories with it. By a stroke of luck he meets Seta, but ends up in a faraway island with the whole cast trying to look for him. (Source: ANN)