"With respect to Secretary - I'm not - I'm a little confused, Senator", Comey replied.
"She was clearly involved in this whole situation... fake news... as you described it, 'big deal, ' took place".
"When I was sacked on May the 9th, there was still an open and active investigation to understand the Russian efforts and whether any Americans worked with them", Comey said until McCain interrupted, again returning to Comey's conclusion in the Clinton case.
None of this seemed to get through to McCain, who kept insisting that Comey had exonerated Hillary Clinton in the Russian Federation investigation, but not Trump.
"I was saying that in the case of the investigation of former Secretary Clinton's involvement, he examined it, said it was over and it was done", McCain said.
In a subsequent statement, McCain blamed confusion on the comments he made at Thursday's Senate Select Committee on Intelligence hearing, which caused an instant commotion on Twitter, on - wait for it - staying up too late watching the Arizona Diamondbacks play baseball.
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But that was not what was coming out of John McCain's mouth.
Comey explained Clinton was cleared because the email server case was "completed", whereas the separate Russian Federation investigation involving Trump affiliates is "nowhere near" complete, so a conclusion can not yet be made.
John McCain's line of questioning for Comey. You reach separate conclusions, ' McCain said.
Despite the investigation's close, Comey told congressional leaders in late October that his agency would look into whether additional classified information was contained in emails sent over Clinton's private email server while she served as secretary of state.
McCain was the last senator to question Comey during the almost three-hour hearing and his line of inquiry left many observers scratching their heads.
McCain said he wanted Comey to answer whether or not Trump's interactions with Comey constitute obstruction of justice.
"That's just a guess, but I've had a lot of conversations with humans over the years", the former Federal Bureau of Investigation chief said.
"I get the sense from Twitter that my line of questioning today went over people's heads".