That’s kind of the point of RICO. If this is a coordinated conspiracy then Trump can’t just say “hey listen my advisors told me this was legal” if those advisors are on tape giving out the details of their criminal conspiracy
As pointed out elsehwere, Stone does not have to be collaborating directly with Trump, but there are still a lot of unidentified co-conspirators, and "other persons known and unknown to the grand jury." There's room for Stone to be in one of those groups.
I find it very hard to imagine that there isn't evidence of this traitor directly plotting with Trump et al. We just haven't seen it yet.
I have no doubts that at some point before the election their was a Coup Plot Kickoff Meeting with at least Bannon, Stone, Treason Trump, and Guiliani in the meeting. I don't know who else was in this meeting, but we know that Bannon and Stone attended the meeting because of their video confessions.