Also add Arunachal and Upper Assam, which while not necessarily a Christian majority, are certainly significantly Christian and growing.

The short answer is that Baptist missionaries spread throughout the region. The Nagas are predominantly Baptist, and NCSN, the major separatist/terrorist/whatever organisation is foundationally Baptist.

This actually goes back to the 19th century with a now-famous missionary named Edwin Clark. He and his wife are now household names among Naga-populated areas (I actually stayed at a house once where the homeowners had a mug showing their faces and dates of their mission work).

Then in addition to this, you have a large population moving across the Patkai mountain ranges into India from Myanmar, people who were converted earlier and brought with them their Christian faith.

Also, Wikipedia says this about Clark:

Although Clark succeeded in converting the Nagas, today the entire Naga community are just name sake Christians and practise their animistic rituals with a little bit of Christianity thrown in.^[citation needed]

But that's not true. The Christians in the region tend to be devout bordering on fundamentalist, the missionaries are credited to this day with ending human sacrifice and head-hunting (though that happened more slowly), and in fact the decrease in local cultural traditions is so widely acknowledged that a Hindu-backed "local" religion called Rangfra has been developed in a specific subset of Nagas as a means to preserve or bring back local practices, or at least that's the narrative.

So that's the short answer. Prior to the 1860s people practiced local indigenous religions, and then Christian missionaries moved in and convinced a huge number of people to convert.