Professor Capek was dead, but... that was not the end of it all.
Strictly speaking, Professor Capek was merely an initiator, there was still no trace of the Silver Dusk Cottage behind him, and there were other participants who were still alive.
The Capek Research Society was initially composed of seven individuals. When Mariabel, one of them, died, the society temporarily disbanded. However, after Shirley joined, the research society still had four members. Now with Professor Capek dead and Shirley unconscious, it indicates at least two others are still within the school.
Afterwards, Duanmu Huai packed up Professor Capek's files, paired the clues and data, and handed them to Chief Reschdorf, temporarily ending this series of serial killings. Chief Reschdorf somewhat breathed a sigh of relief, despite not seeing a body. Assuming Duanmu Huai was accurate, it meant that similar serial murders wouldn't reoccur on the streets of Fog City... The police, too, could finally breathe easy.