Once at the harbor just fight your way to the right through whatever opposition you face. When you reach the second bridge you'll be stopped by Honda. Honda is by far the hardest boss thus far. He has an immense amount of health, and he can also do special pile driver and running clothesline attacks if you get too close to him. He can also do low kicks that knock you to the ground. Once you've dealt with his cronies it should be easier to avoid his attacks. Once he's gone you'll get an impressive 8426 EXP.
Continue to the right, fighting anyone who opposes you. Very shortly you'll find Miho and Yoshihiro. Yoshihiro explains that he got rid of the previous Union president to further his plans for taking over Japan, and that he enrolled at Nekketsu specifically to eliminate Kunio. Kunio insults him, and then you get to fight him. As well as punching and throwing he has a special jump kick as well as a bicycle kick, and he can also fire his pistol—all three of his special attacks can take away a good chunk of your health. In the case of the gun he can only fire it straight ahead, so when you see him reach for it you can just change your horizontal position or just hit him to cancel the attack.
When he's finally defeated Yoshihiro says if he had your power he could control the world, and Kunio retorts that that's not what power is for. You now get Miho with you. Go through the door to the right and she will be reunited with her brother. You'll then meet up with your friends to head back to Tokyo, and the credits roll. The end.