Manny Ramirez’s unexpected absence last night left a large hole in the Red Sox lineup.

AP / Chris O’Meara

BOSTON — The Red Sox’ long, sometimes contentious relationship with Manny Ramirez appears to have reached the tipping point.

After Ramirez yesterday informed the club that he was unavailable for the second time in as many games because of a sore right knee, the team had Ramirez undergo an MRI on both knees.

The MRI came back clean on both, forcing something of a showdown today. With a clean bill of health, the Sox will put Ramirez’s name in the lineup for this afternoon’s nationally televised game against the Yankees. If Ramirez informs the team that he is again unavailable, disciplinary action — which could include a suspension — will be taken.

For the last two months, the Red Sox had been waiting for the day when they could reunite their potent combination of David Ortiz and Ramirez.

But last night, when Ortiz was in the lineup after an eight-week absence, Ramirez wasn’t.

Manager Terry Francona wrote Ramirez’s name into the lineup, which was posted when the clubhouse opened. It was assumed that Ramirez’s knee had improved since Wednesday when the slugger told Francona he was unavailable in Seattle.

But while Francona spoke with reporters in a second-floor interview room, Ramirez informed bench coach Brad Mills that he was again unavailable, necessitating a revised lineup.

“We had him in the lineup and he said he couldn’t play,” said Francona after the Red Sox’ 1-0 loss to the Yankees. “By the time I start with the media (at 4 p.m.), there’s the expectation that guys (posted in the lineup) will play.”

Minutes after being informed that Ramirez was out, Francona appeared on the field as the regulars — minus Ramirez — took batting practice. Francona then summoned principal owner John Henry and chairman Tom Werner. The trio left the field and met behind closed doors in Francona’s office for an extended period. Ramirez joined the meeting for a time.

Skepticism obviously exists within the organization about the severity of Ramirez’s injury.

Ramirez did not seek treatment for the knee on Thursday, an off-day, a signal to Francona that Ramirez would be available for last night’s series opener.

Ramirez said Wednesday in Seattle that the knee had been bothering him for the last week, but he has not sought treatment from the training staff.

Henry’s involvement in all of this could be telling.

Since purchasing the Red Sox in 2002, Henry has been one of Ramirez’s biggest backers and has defended him in the face of many controversies.

But when Ramirez complained to the Boston Herald during the All-Star break that the Red Sox and ownership had been less than forthright with him and he hoped they would be honest in communicating their future plans for him, Henry lost patience.

He fired off am angry e-mail rebuttal to the Herald, telling the paper he found Ramirez’s remarks “offensive,” while contending that the organization has always been honest with Ramirez.

This is not the first time Ramirez has sat out with knee soreness. He played little over the final five weeks of 2006 due to patella tendinitis in the left knee. At the time, MRIs showed some swelling, but no structural damage to the knee. Ramirez rehabbed the knee that offseason and reported to spring training in 2007 without any limitations.

The debate over how hurt Ramirez is comes in the aftermath of two off-field incidents involving Ramirez and others.

On June 5, NESN cameras caught Ramirez slapping teammate Kevin Youkilis, reportedly over Youkilis’ frequent outbursts in the dugout.

Then, late last month in Houston, Ramirez shoved traveling secretary Jack McCormick to the ground. Ramirez had made a late request for 16 game tickets and when McCormick advised him that it might be difficult to fill, Ramirez exploded and pushed him before others could intercede.

Those incidents, along with Ramirez being unavailable for the last two games, may have altered the organization’s thinking on picking up Ramirez’s 2009 option, worth $20 million.

At the start of the season, it seemed a virtual certainty that the Sox would pick up the option for next season, given the lack of power-hitting alternatives on the market and the fact that the Sox need only commit to him for the short-term.

Ramirez, meanwhile, has repeatedly said that he hopes the Sox would offer him a contract extension past the second option year of 2010. Failing that, Ramirez has said, he would like to play elsewhere for at least four more seasons.

Ironically, if the Sox sour on Ramirez further and decide not to exercise the 2009 option — a decision they must make by the first week of November — such a tactic would free Ramirez to auction himself off to the highest bidder for a longer deal, one far more lucrative than the $40 million represented by the two options the Sox hold.

smcadam@projo.com