Pikmin Hybrids has a storyline where Olimar attempts to prevent the Pikmin species extinction. In caves he can find Problems, which are items that hold clues to the Pikmins' decline.
Its a list of food supplies from Olimar's last voyage. Found in Mamuta Garden.
"I must have dropped this food supply list on my second visit to this planet. How did it end up in this cave? The geography of this planet seems to have changed again in my absence. Strange."
It's a dead Pikmin onion. It has a strange black and purple flower on top of it. It is found in the Deeper Trunk.
"I find this very disturbing. Could the death of this onion be linked to the strange candypop buds I've been seeing? I must search out more areas to investigate."
"I can investigate this specimen more closely now that I've found a inactive one. I am certain these new Candypop Buds are killing off the Pikmin. But where did they come from? How do I stop them?"
It's a Hocotation plant. Found in the Molten Beast Haven.
"This grain is highly nutritious and a staple in Hocotation diets. It isn't native to this planet. Louie may have dropped it on one of his treasure missions."
"This horrible behemoth must be the source of all the Vile Candypop Buds! I need to find a way to kill it. The Pikmin race must be preserved! Perhaps I should retrace my steps..."
It's a gold colored berry. After Olimar finds this last note he must acquire seven golden berries and go to the Dark Poison Land.
"Aha! The juices inside this berry can kill Vile Candypop Buds! All I need to do is find seven more of these hidden in caves and I will be able to destroy the 'horrible behemoth'! I won't fail you, Pikmin!