An Irish girl who crossed the Atlantic as a stowaway on a Navy destroyer was on her way back to Ireland today.

''I just want to go home,'' Suzanne Twomey, 16 years old, of Cork told Wake County District Judge Fred Morelock. The judge put her in custody of two Naval Investigative Service agents.

Miss Twomey was put on a flight to New York's John F. Kennedy International Airport and left there at 10:45 P.M. on a flight to Shannon, Ireland.

The girl apparently slipped aboard the U.S.S. Conyngham while it was on a courtesy call in Cork. She was discovered aboard the guided missile destroyer Saturday when it returned to its base at Norfolk, Va.