io.js merged back in to node.js, and since they were so far ahead in version number, node jumped to 4.0 from 0.12.x.

https://nodejs.org/en/blog/release/v4.0.0/

The large version bump is because the Node and io projects have been reintegrating and they needed something that wouldn't be misleading for people coming from either background.

It merged with iojs, switched to semantic versioning.