A Manhattan man is feeling flush with anger after he says he was forced to sit in the bathroom for three hours on a cross-country JetBlue flight.

Gokhan Mutlu is now suing the airline for $2 million for having “mortified, disgraced, degraded and shamed” him by confining him to the can.

Mutlu says the bizarre incident happened Feb. 23, when he was a standby passenger for a flight from San Diego to New York.

He was told the flight was full because a flight attendant was taking the last available seat, but was then told she would sit in the “jump seat” and he could have her seat, 2E, the suit says.

He was issued a boarding pass and took the seat, but got a rude awakening as he began to doze off about 90 minutes into the flight.

That’s when the pilot called him “towards the front of the plane, towards the cockpit, and advised the plaintiff that he would have to give his seat up” to the flight attendant, the suit says.

“The plaintiff was puzzled and asked what was going on,” the filing says.

The pilot told him the “flight attendant wanted to be more comfortable and that the ‘jump seat’ was not comfortable for her.”

Mutlu “asked if he was being directed to surrender the seat issued to him and to take the ‘jump seat’ for the remaining part of the flight, which was about 3 1/2 hours.”

The pilot told him the jump seat was for “for personnel only,” the suit says.

“Even more puzzled and perplexed, the plaintiff asked if the pilot was directing him to stand for the remaining part of the flight,” it says.

The pilot said no – Mutlu should just “go and ‘hang out’ in the bathroom,” the suit says. In the meantime, the stewardess took Mutlu’s seat, “closed her eyes and pretended to sleep.”

When Mutlu began to argue, the pilot “became angry at the plaintiff’s reluctance to go . . . to take his place in the rest room and took a much harsher tone with the plaintiff, advising him that he was the pilot, that this was his plane, under his command, and that the plaintiff should be grateful for being onboard,” the suit says.

Mutlu says he was “imprisoned” in the bathroom for hours, which “seemed like an eternity.”

He was ordered back to his seat when the plane ran into heavy turbulence, the suit says.

“Plaintiff walked back to his seat embarrassed, humiliated, mortified, disgraced degraded and still shocked beyond belief,” and tried “to cover his face” as he walked up the aisle, the papers say.

The flight landed at JFK around 5:30 am, and the pilot stopped him as he was walking out “and asked if everything was okay. The plaintiff replied, ‘No,'” the suit says. The suit seeks money for emotional damages.

A rep for JetBlue said the company doesn’t comment on pending litigation.