What if Visa expires prior travelling to intended country???

1. For my higher studies I had applied for German Visa - some how got rejected (feels like a red ink on progress report - may be more serious than that)

2. Currently doing the higher studies in India itself (TN). I have got VISA (multiple entries / year) to Malaysia as I was planning to go there for my internship. Visa states that I have to make an entry with in 1st 3 months.
Unfortunately I need to be here in india for next 6 months and the visa will expire If I don't make a travel next month.

Can someone give me the best advice on whether I need to make a travel for namekevasthe(just like that) to Malaysia in order to avoid further more red inks?

Why did you not explain your situation to the Malaysian Visa Officer. They could have given you a visa with a start date after 6 months. Best option is to approach the Visa Office again and get the issue cleared. If this fails, then you might have to make a trip to Malaysia. But you might face problems when your visa extension time comes around. They might say that you did not start the course off during the period when your visa was given.

I do not know the exact case for Malaysia, but I do know for Germany that they do not issue a visa for more than 180 days in India for students. Students then have to get to Germany while their visa is valid and their school needs to file a application on behalf of the student for extension of the student visa for the study period.