Mario and his friends are enjoying their time in the jungle when the kuppa troops showed themselves. They have been caught by surprise, so none of them are prepared. Mario was able to escape, but the others aren't as lucky as he. They were caught and there is nothing that can be done. Mario tried to flee because he knows that he can't do anything about it for now. At least, when is safe, he can make some plans and come back later to save his friends. He knows that the battle would be even harder in the jungle since most of the kuppa troops are adapted to the terrain, which gives them the advantage. He needs to get a flower power that he could use to combat the kuppa troops.
The jungle is dangerous and Mario is unfamiliar with it. Other than the kuppa troops, there are wild animals in there which makes the mission even much harder than it is. He can be eaten by wild animals if he won't consider them as a potential danger. Even if they are not evil, they could still harm Mario. The animals that live there just want to live and has nothing to do with King Kuppa, but they can't be taken out of the equation since they are part of the ecosystem.
You are in a whole different world from the usual game and you need to explore the area. Of course, the danger is always there as well as with the other game that came before. In this game, you don't need to get the flower to have the power since you have it right at the start. Your goal is to get to the finish line, so stay sharp and you can get to that safely.