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Almost 90% plead guilty. But, this doesn't necessarily mean they are guilty. Usually the Feds undercharge, say, with 10 years in jail at risk for the defendent, but explicitly threaten to charge much more if the defendant doesn't plead guilty. And, there are so many felonies Americans are guilty of on a daily basis, the Feds have so many options to charge. (See "Three Felonies a Day," and Gorsuch's book "Over Ruled: The Human Toll of Too Much Law." I'm reminded of a horrible abuse of power in a where the Feds charged a fisherman with a violation of Sarbanes Oxley because the number of fish in his boat when he docked allegedly didn't match the amount he had on his boat when inspected. He chose to go to trial, and the Supreme Court eventually exonerated him, saying the Feds had misapplied the statute. The Feds bankrupted that guy, though. It would have been better for him if he pleaded guilty, than to fight an be found innocent.) So, an innocent defendant must choose between risking 40-100 years in jail if he goes to trial...and certain bankruptcy, or maybe 10 years if he just pleads. Most plead. I'm not sure this means justice is done. Comey may fight, but if they treat him like they treat normal Americans, he could be fucked either way. Frankly, I don't expect them to treat him that way, since people will be watching them. Only normal Americans are treated that way.

(I'll let someone more intimately involved with grand juries answer your question. I would assume the answer is, "enough is shown to gain an indictment" if the prosecutor desires an indictment. My crim law professor used to say that grand jury indictments were basically automatic...but I believe he was assuming that the prosecutor in question actually wanted the indictment, and wasn't using the process to clear the defendant and wash his hands of the fact that he didn't want to prosecute.)