The story takes place after Mario & Friends Save YTP 5 left off...
Mario takes a nice relaxing vacation until the giant doom ship arrives and summons the Subspace Army. After Mario cleared them all, The Ship arrives to Hyrule and kidnaps the King! Mario, Link and Sonic must team up and began their new epic adventure... but they must defeat the Three Faces of Evil before heading to the Space Colony ARK and Black Doom in general...
And there is a mysterious figure and his goal is to find Mario and when you reach the part where they fight Black Doom... The Man reveals himself!