His arrest, see also here, comes as a bit of the surprise, as he was always close to the Rwandan army, and his pursuit of the remnants of the genocidal Hutu Interahamwe militias were certainly in agreement with the Rwandan government.

It appears that this might be some sort of quid quo pro, with Congo allowing Rwanda to send in troops to take out the Hutu militias in exchange for neutralizing Nkunda.