Nowadays IR is connected throughout evenly.
But earlier Junction stations were the king.
Junction stations would be connecting the trunk routes with the branch line.
An example of a junction station would be Kiul, once the main line via Danapore was connected. To go towards Bhagalpur from Madhupur side you had to change trains at Kiul.
Similarly...
more... you could change for the Sahibganj branch at Khana/Bardhamaan.
Asansol was the changing point for BNR and Adra from Howrah side.
Bakimmpore (Present Patna) was the changing point for Gaya before Grand Chord.
Similarly you had junctions that joined trunk lines like Itarsi and Moghulsarai.