The idea of prototype pattern is having a blueprint / template from which you can spawn your instance. It's not merely to "avoid using new in Java"
If you implement prototype pattern in Java, then yes by all means override the existing clone()
method from Object class, no need to create a new one. (Also need implement Clonable interface or you'll get exception)
As an example:
// Student class implements Clonable
Student rookieStudentPrototype = new Student();
rookieStudentPrototype.setStatus("Rookie");
rookieStudentPrototype.setYear(1);
// By using prototype pattern here we don't need to re-set status and
// year, only the name. Status and year already copied by clone
Student tom = rookieStudentPrototype.clone();
tom.setName("Tom");
Student sarah = rookieStudentPrototype.clone();
sarah.setName("Sarah");