As usual, it starts out in Edo Town.. It's a really huge town this time, and you can get an overhead view of the town from up on a big hill... Goemon still lives with his parents in this, and the Wise Man is also here.. you have to talk to the parents and a few other characters before a white cat will appear laying on the road. It says its hungry, and when you buy some fish for it, then it starts following you around. This cat is named Kotora, and he follows Goemon around for the entire game. Later, Goemon's dad is in front of Edo Castle, and he gives you the trademark red clothes that Goemon wears for the rest of the series... It seems like each of the dungeons have one of these animal deity spirits that you have to save..
The first dungeon's spirit is a giant white tiger, who is also the father of Kotora, and Kotora seems to be central to this plot somehow. The enemies are an army of samurai/shogun-looking people and they are trying to control or kill these spirits or whatever. The 2nd dungeon's spirit is an "Earth Dragon", as in he is literally made of earth, and the island of Japan is his body. You meet him by diving underwater and seeing a giant eyeball pop out of the ground. The 3rd dungeon's spirit is the tree turtle thing that was also the boss of that dungeon. The 4th spirit is a giant warthog. The 5th dungeon didn't have an animal spirit at the end, but just more plot devices and stuff..
Yae, Ebisumaru, and Sasuke all make appearances throughout this game, but you can only play as Goemon. Yae has a gang of ninjas working for her, and they think Goemon is a bad guy at first and put him in jail.. there's a breakout/stealth sequence similar to in Wind Waker. Later Yae helps you out at various other cutscenes throughout the game.. Sasuke is just kind of there in a few cutscenes, and he helps you find the Wise Man's space ship to get to the enemy's base.. You first meet Ebisumaru in a restaurant, and he helps you progress to the next dungeon in exchange for giving him ALL of your money. At the last part of the game, Yae, Sasuke, and Goemon are now working together for the first time and figuring out where to go next, and they help you get to the final dungeon. The characters that Goemon helped bust out of jail earlier, they also show up again near the end, and they give Goemon his first pipe weapon, which is the strongest weapon in the game so that you don't have to use swords anymore. The final boss reveals his true form after being defeated, and turns out to be a giant floating lion head... I guess he's the 5th of the animal deity spirits?
Yeah, that's about all I can care to remember from the story of this game. Obviously and I wasn't able to keep up with most of it so I'm probably missing like 99% of what went on here.
This game felt very... Final Fantasy-esque, like it felt more realistic and grander in scale than the more cartoony, less serious tone of the other Goemon games. It's not terrible, but the gameplay and dungeon design is just unpolished. The puzzles in this game aren't very fun either. I wouldn't recommend playing this unless you know Japanese in order to properly enjoy the story, because the gameplay by itself doesn't hold up.
Some of the music in this game that I really liked:
Opening sequence: https://www.youtube.com/watch?v=2CxG7tz7Ehg&list=PL9029F0176933C496
Edo town: https://www.youtube.com/watch?v=OzIqPrEftXE&list=PL9029F0176933C496&index=3
Boss battle theme: https://www.youtube.com/watch?v=RgxDz2EGJo4&index=13&list=PL9029F0176933C496
Izumo town: https://www.youtube.com/watch?v=d537eI8v4-w&index=14&list=PL9029F0176933C496