For a huge network of trains, it is possibly difficult(not impossible) to store all the data online and for this reason, Ministry of Railways in India has been publishing a book yearly called 'Trains at a Glance'. While this book is easily available at kiosks in India, there is luckily a pdf version available on the website of the Ministry:
To read this you have to figure out a route which is mostly the two most important stations between which you want to explore connections. While it could be tricky, by using a map like this could help you
You can find a valid route numbername, which will help you arrive at a Table number in Trains at a Glance.
Once you have the number say T-97, you get a beautiful page with all the possible train numbers and theretheir timings, listing down all the stations that fall onenroute. Once you have the routetrain number you can use google to check the entire schedule of that train.
This might be tricky, but this book is time and tested. It helps or rather used to help a lot of people in India who do not have access to the internet. And the fact that my dad's team works on it makes me more proud of it!! :)