There is no feasible way to defeat Skull Kid atop Clock Tower in the last six hours of the three-day cycle. What you must do is summon the Four Giants from the four dungeons around Termina (Woodfall, Snowhead, Great Bay, and Ikana) using the song the "Oath to Order". This will cause Majora's Mask to remove itself from Skull Kid and fly up into the moon, where you must chase after it.
^^Nice description, but if this is your first visit to the top of the Clock Tower, then you have to shoot Skull Kid with a Deku-bubble thingy, causing him to drop you Ocarina. When you reclaim it, you are overcome with memories from your adventures in Hyrule, the most prominent being Zelda teaching you the "Song of Time". In Termina, where the moon is going to crash in a very short amount of time, the Goddess of Time is willing to allow you to go back in time by three days, in order to save Termina, as you cannot do everything within such a limited time span. She uses the Song of Time as her "call", and so by playing it, causes her to rewind time for you, with you and Tatl, your fairy companion, being the only ones that have memory of the previous cycles.