NASSAU, Bahamas — Heartbreaking. Crushing. Devastating.

St. John’s had the game. It had it in the first half. It had it in the second overtime.

It threw it away.

Zuby Ejiofor missed two free throws with 4.1 seconds left in the second overtime and Jeremy Roach’s rainbow 3-pointer dropped in at the buzzer, sending the stunned No. 22 Red Storm to a gut punch of a 99-98 loss to No. 13 Baylor on Thursday night in the opening round of the Baha Mar Hoops Championship.

St. John’s blew an 18-point lead in the first half.

It blew a five-point lead in the final six seconds of the second extra session. It couldn’t make free throws or get a key defensive rebound, and it paid for it.

“That was about as difficult a loss as you can have,” coach Rick Pitino said.

Television replay appeared to show the clock starting late after Ejiofor’s second miss at the line. Roach’s shot was reviewed and ruled good.

“I don’t know what to say; the referees didn’t do a very good job tonight,” Pitino said.

It was a wild matchup of Top-25 teams. St. John’s (4-1) led by 18 points in the first half and by 14 at halftime. Baylor (4-1) was dominant in the second half and most of the first overtime.

Kadary Richmond, who was cramping up late in the game, pulled St. John’s even at the end of regulation and the first overtime but wasn’t on the floor for most of the second overtime.

Even without him, the Johnnies found themselves ahead, leading by five after a Simeon Wilcher 3-pointer with 2:19 left.

But three crucial missed free throws followed, one by Deivon Smith and two by Ejiofor. An early shot after St. John’s beat the Baylor pressure by Ejiofor certainly didn’t help matters.

Bears guard V.J. Edgecombe, cramping like Richmond, hit an off-balance 3-pointer with six seconds to go in the second overtime to pull Baylor within two.

After a timeout, the play was to inbound the ball to Smith with Ejiofor screening his man. But the ball found its way to the big man. Baylor immediately sent him to the free-throw line.

Baylor coach Scott Drew called for a review of the foul, believing Ejiofor may have swung his elbow, and the officials obliged. Pitino didn’t like that.

“I felt at the end of the game that it was highly unethical to go to [instant replay] and ice my free-throw shooter,” the Hall of Fame coach said. “The referees should never let it happen.”

Ejiofor led the Johnnies with 22 points, 10 rebounds and five blocks, and Aaron Scott added 20. RJ Luis had 16 points and Richmond chipped in 14 points and seven assists.

Norchad Omier had 24 points for Baylor, 19 coming after halftime.

This was a lost opportunity, a chance for a resume-building victory over a Final Four contender. Ultimately, there were too many mistakes: 12 missed free throws, 18 turnovers and an inability to protect the defensive glass. Baylor had 22 second-chance points.

“Our toughness with the defensive rebounding — they took the ball away from us when we had it,” Pitino said. “That bothers me. I thought they were fouls. The referees didn’t think they were fouls. Only the film will tell.”

St. John’s will have to regroup quickly after this double-overtime marathon.

Brady Dunlap (quad) isn’t expected to be available and several others could be fatigued.

“They’re going to be disappointed. They had the game in control at the end and the guy made a big shot,” Pitino said. “We missed the free throws, could’ve iced it, it could’ve been over, but it wasn’t. Give them credit.”