Article 12 of the indictment says, “a senior Trump campaign official was directed to contact STONE about any additional releases….” This wording suggests that someone higher than a senior campaign official ordered that campaign official to contact Stone about WikiLeaks.
Although Mueller did not charge Stone with conspiracy, the groundwork for additional charges including conspiracy with Russia, was included. One of the perjury charges, for instance, says, “in the course of his [House Intelligence Committee] testimony, STONE made deliberately false and misleading statements to the committee concerning, among other things, his possession of documents pertinent to the Committee’s investigation [of Russian collusion with the Trump campaign].”
Mueller indictment of Stone on these charges may be intended to pressure him to provide evidence against someone higher up, namely Trump. Although Stone swore he would not flip on Trump, he may be expecting a pardon. If Trump doesn’t pardon him, the likelihood of spending the rest of his life in prison may cause him to flip.