Manipur is not the most disturbed state of North East India. But it’s always in the news more often because of road blockades. There are dozens of small secessionist movements across NE India. Manipur in particular has two major issues:
It joined India in 1949 October 15th. That was 26 months after most states and provinces became a part of Indian Union. It is one of the few states that took time to join Indian Union after the British Rule ended. The most important reason being the debates internally as to whether joining India is in its interest or not. Some however opposed it. So the problems started right from 1940s. In 1972, Manipur was declared a separate state. Still the problems from some tribes continued. In 1980, Manipur was declared a disturbed area, and Armed Forces (Special Powers) Act was applied. This led to more violence from disgruntled elements in Manipur. That continues till date. But, overall the state is conducting business for most part, like other states. Occasional violence shows up in Manipur here and there. The most current one from 2015 is related to the demand to keep non Manipuri’s from owing land in Manipur.
Since Nagaland, the northern neighbouring state of Manipur, has similar violent group issues, it gets complicated. North East India has numerous tribes from ancient times itself. There are dozens of languages, might even be in hundreds. Most are in danger of extinction now. The tribes have historical fights among themselves. Since Nagaland issue popped up, an armed group called National Socialist Council of Nagaland came up. This later split into multiple groups. Two of those groups, Isakmuivah and Khaplang started fighting in Manipur. The Kuki tribe of Manipur started feeling the heat. So they started forming their own armed group. Soon four other Manipur tribes started following Kukis. Now it has reached a state where the government has to fight many of these armed groups. Most have either stopped violence, or gone underground. Still, it would take time to bring 100% peace in this region, that has centuries of animosity between tribes.
Lastly, the Demographics, the Bandh culture and Alienation from rest of the India add upto the political drives in the state of Manipur.