We already know that the Times story started off by saying Hillary was under criminal investigation and then moved on to say, no it wasn't Hillary, it was the State Department. But Eichenwald just shreds everything in the story, top to bottom, with such ferocity it made me cringe.

It's impossible to sum up everything Eichenwald says, but he goes through the documents cited by the Times one at a time and shows how the reporters (intentionally) took parts out, ignored elements that misrepresented what sentences meant, put unrelated paragraphs next to each other to make it seem like they were connected when they weren't and on and on.
A few choice examples:
The piece is wrong in all of its implications and in almost every particular related to the Inspectors Generals’ conclusions. These are errors that go far beyond whether there was a criminal referral of Clinton's emails or a criminal referral at all. Sources can mislead; documents do not.
For example, Eichenwald quotes the document and shows how it wasn't about Clinton at all, but about how officials at the State Department now are handling requests under the Freedom of information act.
This is about the process being used by FOIA officials in reviewing former Secretary Clinton. And, former government officials have nothing to do with how FOIA officials deal with requests for documentation. To jump from this fact to a conclusion that, somehow, someone thinks there is a criminal case against Clinton (the original story) requires a level of recklessness that borders on, well, criminal behavior.
Eichenwald's belittlement goes to the level of making fun of the Times reporting.
Yes, there is memo after memo after memo, which the Times preens was given to it by a senior government official (for those who have thoughts of late-night meetings in parking garages or the Pentagon Papers, they were unclassified documents. Reporters obtain those kind of records through the complex, investigative procedure of asking the press office for them.) And all of them are about the exact same thing: the process being used by current FOIA officials reviewing the emails of a former official is messed up. That’s like criticizing the former owner of a car for the work conducted by the mechanic of the new owner.