Mueller lays out the facts to support and defend the entire Russian investigation, but here is the portion that refers to Roger Stone courtesy of WaPo:

The jury ultimately convicted Stone of obstruction of a congressional investigation, five counts of making false statements to Congress and tampering with a witness. Because his sentence has been commuted, he will not go to prison. But his conviction stands.

Russian efforts to interfere in our political system, and the essential question of whether those efforts involved the Trump campaign, required investigation. In that investigation, it was critical for us (and, before us, the FBI) to obtain full and accurate information. Likewise, it was critical for Congress to obtain accurate information from its witnesses. When a subject lies to investigators, it strikes at the core of the government’s efforts to find the truth and hold wrongdoers accountable. It may ultimately impede those efforts.

We made every decision in Stone’s case, as in all our cases, based solely on the facts and the law and in accordance with the rule of law. The women and men who conducted these investigations and prosecutions acted with the highest integrity. Claims to the contrary are false.

That last part is definitely directed at Donald Trump who tweeted this about Stones’s conviction:

Robert Mueller has had to sit back and listen as Trump attacked his integrity, the integrity of his friend James Comey, and the integrity of the entire Russian investigation and said nothing. 

However, when Trump commuted Roger Stone’s conviction, that proved to be the straw that broke the camel’s back.