One charge has to do with Mr. Shkreli having undisclosed control over a huge portion of Retrophin shares. Prosecutors say he handed these shares out to people, including employees, but told them what to do with the shares. He then made it look as though the employees did not work for Retrophin or MSMB anymore, so they could claim they were not affiliates of the company, even though some were actually still working for Retrophin or MSMB, prosecutors said.

Regarding another charge, the defense had argued that Mr. Shkreli did not know he needed board approval from Retrophin to send out settlement agreements, which had Retrophin compensate MSMB investors who had lost their money. But the emails show him fine-tuning the settlement agreements and telling his lawyer, in August 2013, that “there were serious faults with the agreements including lack of board approval.”

The defense has raised credibility issues with some of the witnesses, including showing that Retrophin board members never read one of the proposed consulting agreements in question, and that another man portrayed by the government as a fake consultant might have done real work for the company, at least in Mr. Shkreli’s view.

Mr. Shkreli’s aggressive personality had been largely kept out of the trial, but it came through in the final round of emails shown by prosecutors. “Why can’t you do your job? It is incredible…” Mr. Shkreli wrote to his lawyer, Evan Greebel, who is also charged in the case and will be tried separately in the fall. “You’re inept,” he continues. “Ure done.”

And in an August 2013 email to Retrophin’s chief financial officer, who wrote that Retrophin’s accounting firm had an issue with how the settlement agreements were handled, Mr. Shkreli responded: “FIX THE ISSUE,” adding an expletive before “issue.” “THERE IS NO ISSUE. HOW MANY TIMES DO WE HAVE TO TALK ABOUT THIS”

Until this week, the case had been, in some respects, a fun-house mirror version of a normal fraud trial.

The people presented by prosecutors as Mr. Shkreli’s victims actually made money, for one thing. The defense, usually eager to limit prosecution witnesses’ testimony, had pushed the prosecution to call more victims.