According to the book by Steven M. Gillon The Kennedy Assassination — 24 Hours After via huffpo:
It was standard practice for the plane to take off as soon as the commander-in-chief was onboard. Even after McHugh had ordered the pilot to take off, however, “nothing happened.” According to the newly declassified transcript, Mrs. Kennedy was becoming desperate to leave. “Mrs. Kennedy was getting very warm, she had blood all over her hat, her coat…his brains were sticking on her hat. It was dreadful,” McHugh said. She pleaded with him to get the plane off the ground. “Please, let’s leave,” she said. McHugh jumped up and used the phone near the rear compartment to call Captain James Swindal. “Let’s leave,” he said. Swindal responded: “I can’t do it. I have orders to wait.” Not wanting to make a scene in front of Mrs. Kennedy, McHugh rushed to the front of the plane. “Swindal, what on earth is going on?” The pilot told him that “the President wants to remain in this area.”
McHugh, like most members of the Kennedy entourage, did not know that Johnson was onboard. They believed that the new president was on his own plane flying back to Washington. If LBJ was on the plane, McHugh wanted to see for himself. Since he had not seen Johnson in the aisle — and at 6’4″ Johnson would be tough to miss — McHugh assumed that he must then be in the bedroom. When he checked there Johnson was nowhere to be seen. The only place on the plane he had not inspected was the bathroom in the presidential bedroom.
What McHugh claimed to have witnessed next was shocking. “I walked in the toilet, in the powder room, and there he was hiding, with the curtain closed,” McHugh recalled. He claimed that LBJ was crying, “They’re going to get us all. It’s a plot. It’s a plot. It’s going to get us all.'” According to the General, Johnson “was hysterical, sitting down on the john there alone in this thing.”
I soon discovered that McHugh had told a similar story when he spoke by phone with Mark Flanagan, an investigator with the House Select Committee on Assassinations (HSCA). Ironically, McHugh gave the interview to the HSCA a week before he sat down with the Kennedy Library in May 1978. “McHugh had encountered difficulty in locating Johnson but finally discovered him alone,” Flanagan wrote in his summary to the Committee. Quoting McHugh, the investigator noted that the General found Johnson “hiding in the toilet in the bedroom compartment and muttering, ‘Conspiracy, conspiracy, they’re after all of us.'”