National Investigation Agency judge P Sasisdharan sought clarification of certain points raised by both prosecution and defence during their arguments.
The verdict in the case is expected soon.
The court has examined over 300 prosecution witnesses, four defence witnesses, over 950 prosecution documents, nearly 30 defence documents and 227 material objects in the case during its trial which started in July 2013.
A total of 37 people, including six persons who are absconding, have been named in the charge sheet in the case.
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According to the charge sheet, the accused persons hatched a conspiracy to attack Thodupuzha Newman College Professor Joseph.
He was attacked and his right hand chopped off, allegedly by activists of a fundamentalist outfit on July 5, 2010, accusing him of hurting religious sentiments of a community through a question paper he set for his students.
A magistrate court in Idukki has exonerated Joseph of the charge of hurting religious sentiments.