Team Big does not have one fixed location; Big lives in Mystic Ruins North, Honey inhabits Sunset Park Zone (but is more often than not at Station Square and Metropolis performing retail therapy), Tikal squats on Angel Island and Marine spends her hours in the aquatic strip from Aqua Lake Zone to Aqua Planet Zone and the underneath of Troll Bridge Zone.
The storyline kickstarts with Big fishing on the Mystic Ruins North/HydroCity border when Froggy escapes. As furious as the docile beast can be, he gives chase, and the fishing stage HydroCity begins. After being caught, Froggy escapes again and runs towards Sunset Park Zone. An action stage of that zone begins, and then we see a cutscene where we see Froggy fast asleep on top of Honey; Big's thudding wakes Honey up, and seeing Froggy on top of her, she screams. After an extended conversation - quite obviously involving an apology - the two cats become friends. Their chatter does not remain uninterrupted, however, as Tikal arrives complaining that the Master Emerald has been broken again. An appropriate mother's meeting ensues until Marine the Raccoon, as acerbic as ever, comes bickering of a raucous racket (the Emerald being smashed). After a while, the sun descends, so the four of them actually decide to sleep on the problem.
Not an easy task for a certain acerbic someone. Marine, in no small part owing to how irascible she is over the explosion of the Master Emerald, can't sleep, and once all other parties are awake the next morning, she complains about a racket seemingly happening down under. Honey dismisses this as paranoia and decides a spot of retail therapy is in order; however, when the four of them reach Mystic Ruins North - to get the train to Mystic Ruins South, which is adjacent to Metropolis and thus Station Square - they find that the train isn't in operation, so they are forced to walk. Zones Marble Garden Zone, Casinopolis and Aquatic Ruins are played consecutively and then split up; Big does his own thing (fishing in Aquatic Ruins, possibly Oil Ocean Zone) while HMT perform their retail therapy. Here, fishing stage Aquatic Ruins plays.
At the end of this stage, HMT arrive back with a newspaper marked "Trains fail for second time in a row, cause under investigation". Team Big decide to investigate. The team go to Mystic Ruins North, and find that some holes have been bored into the walls of the station at the back. They are contemplating whether or not to enter, when suddenly Egg Pawn boosts out of the tunnel and straight into Big, causing him to fall straight over. After a discourse on what the fuss is about and why the quadrumvirate should tackle the issue, Team Big decide to interrogate the cavern. They follow the path about three quarters of the way out, whereupon the caverns end is lit right up. At closer inspection, they see Team Covert running through a staircase damaged badly by (what appears to be) an explosion and then follow them up. When they hit the top, however, there is no sign of Team Covert; what they find is a severely damaged surface of Sunset Park Zone. They decide to head backwards, and quickly pilot the train back to Mystic Ruins South in the form of a mini-game. Upon arrival, they are greeted with a hero's welcome and congratulations of all currently at Metropolis. After an extended appraisal, the team head back to Sunset Park Zone via train to Mystic Ruins North and then on foot the rest of the journey; once at the end of Mystic Ruins, a version of HydroCity begins played with a slightly lower tide than usual. Once at the end, they meet Egg Pawn again, with a final request; find out what the cause is for the additional racket in Underground. HydroCity is played again, but as an adventure field in which the team chat. At the end of this, they find footsteps, and once they hit the underground Team Underground bolt forward and complain that a group of individuals have been causing massive amounts of disruption. Still bound by their agreement to Egg Pawn, and with the well-mannered Tikal again overriding Marine, the team decide to investigate. Action stages Mystic Ruins, Gigalopolis, Sleeping Egg Zone, Mecha Green Hill Zone and Electric Egg Zone play.
Immediately afterwards we zoom into a cutscene in which Team Big are walking down the tunnel formed by the linking of Electric Egg Zone and Crystal Egg Zone. On their way to Crystal Egg Zone, they see that what looks like a freshly dug cavern has been made into the side of the tunnel. Honey decides to look down there, but for Big to lead just in case of an emergency. This proves to be the team's downfall; Big's heavy footing alerts the inhabitants of Labyrinth Zone, Team Covert (again!) of their presence. But instead of bolting, like before, Covert, the team's leader, decides enough is enough and begins arguing. A boss fight against the team ensues, after which the team run as quickly as they can away from the underground. Action stage Spring Yard Zone plays, which will take the team to Mystic Ruins South and to Mystic Ruins North via train, whereupon they explain to Team Underground the situation. Their final movement is to go through the adventure field HydroCity and back down into Sunset Park Underground and explain the situation to Egg Pawn.
Marine and Tikal act as Honey's conscience; Marine is acerbic and self-centered and Tikal is compassionate and polite.