Naruto: Ultimate Ninja Heroes offers quite a few options of gameplay. The main mode, Heroes Mode, is basically the game's story. While it doesn't strictly follow the events of the series, it basically takes you to just before the Chunin finals and through the destruction of the Hidden Leaf Village. This mode is very different from the console version's Ultimate Road. Here, you will chose a team of three characters (you can choose preset teams or make a custom team) and take part in a series of fights in an endurance or survival fashion. Each fight starts off with you choosing the order that you want to use your characters in. If your current fighter is defeated, the match restarts with the next person in your queue. Whoever wins the fight gets a little bit of their health back (including the opponent if they win) and once you clear a stage, all of the characters on your team gain some health and chakra. So this means that even if you have two of your characters defeated in a battle and your last fighter is all but gone, beating the stage will give them all some health and give you a sporting chance.
Teams and characters also have abilities that you can use before the fights start. These are modifiers you can use to help even the playing field. Some moves can be used on your team (like health, chakra, attack or speed increases) and others can be used on your opponents (basically the same modifiers, just decreases instead increases). Also, some moves can be used on an entire team and others are for individuals. You are given a pool of moves to use throughout the entire series of battles so you will want to ration them out accordingly.
Once you have completed a story-arc with a team, you will unlock the next arc (and difficulty level), be awarded points and collectables and get to try the same matches with a different team or go on to the next set of stages.
Promotion Test lets you take characters into a series of missions (which are unlocked by completing various modes in Heroes Mode) and increasing your rank. You will graduate from a Genin, to Chunin, Junin and eventually Ambu Black Ops. With each rank, the missions you will need to complete in order to graduate to the next level don't necessarily get more difficult, just more numerous. You just need to finish three missions in order to move from the Academy Student to Genin and four missions to go to Chunin. But along with an increase in rank, you will be able to participate in certain ranked missions. All of these battles (both in Promotion Test and Heroes Mode) let you earn points that can be used to modify characters' skills in the Parameter Power-Up Menu Option.
VS CPU Mode and Wireless Mode are both one-on-one matches, just one is against A.I. and the other is against a real opponent (over the internet). In Wireless Mode, you can also trade profiles with players that are in the Waiting Room or start a game sharing session with someone standing next to you who doesn't have a copy of Ultimate Ninja Heroes.
Naruto's House is where you will go to view all of the videos, images and songs that you unlock by playing Hero mode. This feature is carried over from the other two Ultimate Ninja games.