The filing in Centre County court said the suit contains "sundry misdirected complaints" and argued that the plaintiffs don't have standing to challenge the consent agreement between the NCAA and Penn State over the child molestation scandal involving ex-assistant coach Jerry Sandusky.
"Plaintiffs resort to tortured interpretations of the NCAA bylaws and the case law in an effort to obscure two inescapable facts: they are the wrong plaintiffs and they have sued the wrong defendants," the NCAA wrote.
The lawsuit was filed by the Paterno estate, a few trustees and faculty members, nine former players and two former coaches, including Paterno's son Jay Paterno.
The NCAA said Paterno's estate was not able to say how its commercial interest in his reputation lost value.
"The NCAA is left to guess whether the estate has some cache of autographed footballs that coach Paterno signed before his death but, presumably, were not sold in the seven months between his death and the publication of the consent decree," the NCAA said.
Messages left late Thursday for lawyers for the plaintiffs were not returned.
The NCAA filing said the lawsuit did not meet legal thresholds for breach of contract, defamation, commercial disparagement, interference with contracts or civil conspiracy.
Sandusky, 69, is serving a 30- to 60-year prison sentence after being convicted last year of 45 counts of child sexual abuse. A state appeals court recently heard arguments as he seeks a new trial.
The NCAA and Penn State entered into the agreement last summer, requiring the school to pay a $60 million fine and endure a four-year ban on post-season play. It also voided 112 wins from Paterno's final years. Earlier this week, the NCAA announced it would gradually restore the 20 football scholarships that also were taken from the school as part of the deal.
"Plaintiffs are obviously deeply disappointed with the consent decree and its effect on the legendary football program that they love," the NCAA wrote. "But plaintiffs cannot cobble together a sustainable lawsuit from their sundry misdirected complaints, however sincere their disagreement with the agreed resolution of the Jerry Sandusky matter."
If the lawsuit succeeds, the NCAA said, it would make it impossible for the organization to ever enter into a consensual resolution of a rules infractions matter, even if the university and the NCAA agreed on it.