Just hours away from departing Washington for the World Economic Forum in Davos, Switzerland, Trump -- already dressed in his overcoat -- stood up from the Resolute Desk, strode out of the Oval Office and made his way to Kelly's office, where he upended an immigration briefing with a room full of reporters for the next 10 minutes.
It was, as one source would later describe, "a warning shot" from a freewheeling President who has felt more and more undermined by his structured chief of staff.
For Oval Office watchers, a familiar film reel is playing on the screen: An irritated president. An outspoken chief of staff. A missed trip.
Kelly was in the middle of a story when Trump entered the room, to the surprise of reporters and White House staff. It was a rarity for a President who hardly ever enters staffers' offices. Typically, when someone wants to speak to Trump, they go to him.
"Hello everybody, how's he doing, OK?" Trump asked Wednesday night, speaking of Kelly.
"I think by the way he's doing great. He's doing great. Fake news yesterday, or two days ago. I rarely put out a tweet, praising somebody, but only when they get a false story."
The impromptu press conference set off a scramble inside the White House press shop, with staffers were left wondering: "What just happened? What do we do? What did he say? And was it on the record?"
Though White House staffers insisted to CNN that he coordinated his drop by with Kelly beforehand, Trump, already frustrated with the idea that Kelly is managing him, put him "in a box" once the briefing ended, according to a source familiar with the interaction.
Trump then boarded Air Force One for the 9-hour flight to Davos, while Kelly remained behind in Washington to work on immigration reform.
The flare-up was just the latest episode that highlights how the relationship between the two has evolved since Kelly was brought in to replace Reince Priebus last July. Trump has been privately annoyed with Kelly since his interview on Fox News last week when he said Trump had "evolved in the way he's looked at things." The interview set Trump off -- he "hated" his comments, one person familiar with his mood told CNN, and spent the evening calling friends and allies to complain about it. Trump later insisted that his relationship with his chief of staff is fine.
Sources who are close to the President say he feels Kelly doesn't respect him, and only pays him lip service. Aides have privately wondered about how dismissive of Trump Kelly is when he is out of earshot, noting that Kelly has told colleagues he is incredibly media savvy and has bragged about the positive coverage he received when he worked for the Joint Chiefs of Staff.
Kelly has been extremely careful to avoid giving the impression that he is somehow managing Trump -- which people close to him say is a conscious effort.
Trump's frustration with Kelly is evident, but some sources caution that talk of discord is planted by Trump loyalists who have seen their access to the President dwindle in light of Kelly's strict policies.
Two of his harshest measures -- screening all of the President's incoming calls on the White House switchboard and denying those outside the administration access to the White House grounds -- have irked associates who work in the private sector and rely on their ability to boast about access to the President.
Though Trump insists his relationship with his chief of staff is fine, some wonder if Kelly could face a similar fate to his predecessor. Though Priebus initially accompanied Trump on all of his trips, he stayed behind in Washington more often at the end of his tenure.
When Trump flew to Germany for the G20 summit, Priebus stayed behind to work on health care. He was replaced later that month.
One source cautions that Kelly staying back could be more about being productive because staffers often find it easier to work when the President is away.
But Trump has a growing feeling that Kelly is trying to quietly signal to people outside the White House that he is here to protect the country from him, sources familiar with the President's thinking said.
Trump often becomes vexed when staffers are given credit for his accomplishments. Once he sees a staffer as getting out in front of him -- as Kelly did with his remarks on Fox News -- the President gets his back up.
Those close to Trump believe the stunt he pulled at the briefing with reporters Wednesday night was "a warning shot" to Kelly, meant to serve as a reminder of who is boss.
And for some, it signals a sign of things to come.
"This is casebook," one source told CNN. "The man has to eat his own."