Sebastian knows about Jim's plan and he also knows there's a huge possibility of Jim killing himself in the process. Problem is, as much as Sebastian is loyal to what Jim does, he also cares about him and won't just stand there letting him die. Maybe they have a verbal fight (probably not unlike John and Sherlock) and, as Sebastian can't trust anyone among their people with what he intends to do, he finds John and approaches him instead. Sebastian respects another strong ex-army man, whom he has a common goal with, so he shares some important information with him. It's up to the two of them to stop the Fall and make sure both Jim and Sherlock live.

I prefer established (but maybe on and off) relationship between Jim and Seb, and pre-relationship with mutual pining between John and Sherlock.

Bonus: for Jim Seb is lot like John for Sherlock, and Jim is bad at taking care of himself. Sebastian has to make sure Jim eats and sleeps (takes his meds, at least sometimes?). Maybe he knows Jim's embarrassing secrets, something very personal.