In his highly anticipated testimony before the Senate Intelligence Committee on Thursday, Comey discussed the bureau's investigation into Clinton's use of a private email server, noting that he thought it was odd of Lynch asking him to call it a "matter".
Comey pointed out they were separate investigations, begun at different times.
Following the hearing, McCain acknowledged that his questions "went over people's heads", joking that the inquiry was affected by an evening spent watching the Arizona Diamondbacks. He seemed to be arguing that Comey exonerated Clinton, in a sense, but left an investigation looming over President Trump, setting a double standard.
"Because I have been very loyal to you, very loyal; we had that thing you know", Comey quotes Trump as saying, as part of a request that Comey state publicly that Trump himself was not under investigation.
The email controversy dogged Mrs Clinton's presidential campaign.
Back when the server story was still unfolding, Cornyn called for Comey to launch a full investigation with its own special counsel, similar to the role that Robert Mueller is playing in the FBI's Russian Federation probe.
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"At least in the minds [sic] of this [committee] member there's a whole lot of questions remaining about what went on, particularly considering the fact as you mentioned it's a quote big deal, as to what went on during the campaign. In other words, we're complete in the investigation and anything that former Secretary Clinton had to do with the campaign is over and we don't have to worry about it anymore?"
The Republican National Committee and GOP lawmakers highlighted Comey's revelation about Lynch after the hearing, but Kaine said they should focus on the ongoing investigations into Russia's role in the 2016 election.
He confirmed Loretta Lynch wanted him to call the Clinton investigation a "matter" to downplay it.
One of the oddest moments of the day came from Arizona Senator John McCain.
McCain said he "missed an opportunity" to ask a pointed question in today's hearing but would clarify his question and submit it to Comey in writing.
McCain said he was trying to see if Comey would apply the same approach in the case of his conversations with President Trump, and make a public determination into whether President Trump's conversations with Comey constituted obstruction of justice.