As the final seconds wound down, the students behind each basket serenaded the home team with their haunting “Rock Chalk Jayhawk” chant, marking another victory over Baylor, which has never won here, and cementing another perfect season at home — the 20th since Allen Fieldhouse opened in 1955.

It was all so familiar and yet, as virtually everyone in the building could sense, it was not.

The hulking junior center Udoka Azubuike, as potent a post player as there is in college basketball when healthy, has been lost for the season because of torn ligaments in his right hand. The deadeye guard Lagerald Vick, the team’s only senior — and a starter on last year’s Final Four team — returned home to Memphis several weeks ago for personal reasons and will not return. Forward Silvio De Sousa, who practices with the team and sits on the bench in street clothes with Azubuike during games, has been barred from playing by the N.C.A.A. since a shoe company consultant testified in October that he funneled money to De Sousa’s guardian.

What has given this season a darker tint, though, is the uncertainty about what fallout lies ahead from the F.B.I. corruption investigation that has roiled college basketball, ensnaring not only Kansas but Louisville, Arizona, Louisiana State, Oklahoma State, Southern California, Auburn and North Carolina State, among others.

Kansas took its uncomfortable turn in the spotlight last October when T.J. Gassnola, a basketball consultant for Adidas, which has a 12-year, $191 million apparel contract with the university’s athletic programs, testified in a Brooklyn courtroom that he had arranged payments to the families of two Kansas players.

Though Gassnola said he never told Kansas Coach Bill Self about the payments, lawyers for the former Adidas executive James Gatto on trial pointed to text messages between Gassnola and Self and a Kansas assistant, Kurtis Townsend, in which Gassnola pledged his help in landing players.

Another trial, for bribery charges against three defendants in the corruption case, is set to begin in April, shortly after the Final Four.

Self said the revelations in the case, which the N.C.A.A. is investigating, have not been troublesome to his players — other than De Souza, who the university has argued is being punished unjustly — but acknowledged that the developments have hovered over the coaching staff and will continue to do so. He called the case “draining.”