The episode also underscored the difficult challenges that even a four-star general faces in instilling a sense of order around Trump, whose first instinct when cornered is to lash out, even self-destructively.
By today, Trump, back at his New Jersey golf club, was further isolated and the White House was again under attack.
Some aides and confidants privately described themselves as sickened and appalled, if not entirely surprised, by Trump's off-the-cuff comments. And the President watched, furious, as a cascade of chief executives distanced themselves from him, prompting the dissolution of his major business advisory councils.
Kelly allies say the former Homeland Security Secretary came into the West Wing job clear-eyed and practical, with the goal of implementing discipline on the staff and processes of the White House, not controlling the President himself.
"It's clear Kelly is having a stabilising and organising influence on the White House," said Newt Gingrich, a former Republican House Speaker and informal Trump adviser. But, Gingrich added, "He will gradually have an impact on Trump but it won't be immediate. There are parts of Trump that are almost impossible to manage."
Another Republican operative and unofficial White House adviser was more definitive, saying that no matter how respected or talented Kelly may be, his first 2 1/2 weeks on the job demonstrated an essential truth about the Trump White House: The President will act as he so pleases, even in spite of - and sometimes to spite - the efforts of his aides.
"The Kelly era was a bright, shining interlude between failed attempts to right the Trump presidency and it has now come to a close after a short but glorious run," the operative said.
"Like all people who work for the President, he has since experienced the limits of the President's promises to cooperate in order to ensure the success of the enterprise."
This portrait of the White House under Kelly comes from interviews with 17 West Wing aides, informal advisers, Republican lawmakers and Trump confidants, many speaking anonymously to offer a more candid assessment.
During Kelly's short tenure, Trump has startled the world with his bellicose rhetoric on North Korea and attacked Senate Majority Leader Mitch McConnell, furthering imperiling his already stalled legislative agenda.
Nonetheless, Kelly has so far largely improved staff morale, and implemented a rigor and order that has left West Wing aides feeling both more optimistic and less mistrustful of one another, according to several White House aides.
He has been empowered to shake up the staff, if necessary, though one confidant noted that so far, all Kelly has done is restrict access to Trump. The chief of staff is currently doing a thorough review of everyone's portfolio, and this friend noted there may be more West Wing consternation when Kelly begins reallocating assignments.
Longtime Trump campaign associates have found themselves out of the loop and unable to build a rapport with Kelly. He has shown little interest in courting them or in seeking out their advice about how to improve the President's standing. Phone calls go unreturned or handled in a friendly but curt fashion by his top aide, Kirstjen Nielsen, who came over with Kelly from Homeland Security, they said.
Hope Hicks, one of the President's most loyal and trusted advisers, has been elevated to the role of interim communications director - a role she has unofficially occupied for some time.
In the week before Trump departed for an August holiday in Bedminister, New Jersey, the entire West Wing team began showing up at the 8am senior staff meetings. Even Trump's daughter Ivanka - who rarely if ever appeared at staff meetings led by Reince Priebus, the previous chief of staff - began regularly attending.
Kelly also transformed the West Wing from a political Grand Central Station - with aides and hangers-on cycling through the Oval Office - into an actual place of business. One outside advisor recalls stopping by the White House to say hi to his friends on days he had free time. Under Kelly, he said, approvingly, "If you're coming now it's, 'Why are you coming? Who are you coming to see? And why does the White House care about what you have to say?"
Aides usually work through Nielsen, and she funnels information to him, who then decides what to show the President.
One key difference between Kelly and Priebus, said two White House officials, is that aides respect Kelly and feel his efforts to control the information flow to Trump are about better serving the President - not self-preservation.
Nonetheless, Trump has shown signs of chafing. Despite Kelly's switchboard requirement, the President has used his personal cellphone to reach people. And one person close to the President described him as a "caged animal" under Kelly, saying he is always going to respond negatively to attempts to corral him or keep him on a script.
The President was upset by the almost uniform backlash to his initial statement on Sunday on Charlottesville, in which he failed to condemn the white supremacists and neo-Nazis by name and decried violence from both sides.
Although he did offer a broader scripted condemnation on Tuesday, the President yesterday reverted to what aides and confidants say are his more authentic views, arguing that both sides were to blame for the Charlottesville violence.
Gary Cohn, Trump's top economic adviser, who is Jewish, appeared with Trump at yesterday's news conference, standing behind the President in the lobby of Trump Tower as he suggested there were good people who protested alongside the white supremacists and neo-Nazis who organised the rally. Those close to Cohn described him as "disgusted" and "frantically unhappy," though he did not threaten to resign.
But Trump himself felt vindicated after the remarks, according to people familiar with his thinking. He believes that his base fully agrees with his assertion that both sides are guilty of violence and that the nation risks sliding into cauldron of political correctness.
On Capitol Hill, Kelly's evident lack of an ideological compass has drawn mixed reactions from Republicans who have dealt with him, according to lawmakers and aides.
Republican leaders appreciate Kelly's light touch so far on strategy and planning for a busy September. Instead of dictating terms, he is listening to their mounting concerns about legislative expectations and assuring them that he will be a partner and not a foe.
But some of Trump's conservative allies said they wish Kelly would do more to force the Republican establishment to rally behind Trump and were worried that Kelly was following the model of Priebus by showing too much deference to congressional Republican leaders.
Members of the conservative House Freedom Caucus have talked about Kelly as a "black box" who is unreadable on policy, several people close to the group said.
