Despite a series of recent setbacks, prosecutors said on Tuesday that they intend to retry a Brooklyn man in the 2003 murder of a New Jersey college student, setting up another courtroom battle in a case that has already seen a two-week trial, numerous appeals and countless hearings.

In February, the long-running legal saga of the man, John Giuca, was upended when a state appeals court tossed out his guilty verdict, ruling that the Brooklyn district attorney’s office withheld evidence from his initial lawyer and relied on testimony from a witness who lied during the murder trial in 2005. Twenty-one at the time, Mr. Giuca was convicted with a friend, Antonio Russo, of killing the student, Mark Fisher, after a raucous night of drinking in Manhattan ended at a party at Mr. Giuca’s home in Prospect Park South, Brooklyn.

Now 34, Mr. Giuca maintained his innocence throughout more than 13 years in prison, and in the months he has since spent in jail on Rikers Island, where he was moved after the appeals court threw out his conviction. In the wake of the appellate ruling, prosecutors said they still believed he was guilty and had enough evidence to convict him again. At a hearing on Tuesday in State Supreme Court in Brooklyn, the prosecutors repeated that position, adding that even now — 15 years after Mr. Fisher’s death — they were continuing to investigate the case in preparation for a second trial.

Mark A. Bederow, a lawyer who has handled Mr. Giuca’s serial appeals, has already cast doubt on the district attorney’s chances at a second trial. In court on Tuesday, he repeated his own position, saying that the prosecutors on the case were “sitting three months later in an even weaker position than in February.” One of the witnesses the prosecution called at the first trial, a jailhouse informant named John Avitto, was discredited by the appeals court, Mr. Bederow noted. Another potential witness, Angel DiPietro, a then-college student who left the house party not long before Mr. Fisher was killed, has an unusual conflict of interest, he said: She now works for the district attorney’s office.