There are lots of food pellets near the ship, and there is only one part left, but don't get sidetracked because there is a lot to do in this region. This is a good place to come back to later though if you have an extra day and just want to build up your Pikmin numbers. The first thing to deal with is a boss, and which boss you get depends whether it's an even or odd number of days since impact.
Start with at least 20 Yellows, 20 Reds and as many Blues as you need to get to the 100 Pikmin limit. Head north through the gap where the cardboard box was, then left over the box into the large circular area. Getting 100 Pikmin through these obstacles at once is tricky so you might want to make more than one trip. A new enemy you may meet on the way is the iridescent flint beetle, which looks just like its name. It won't hurt your Pikmin but they are irresistibly driven to attack it, so you may have to call them a few times to keep them in line. If you have the time, try throwing some Pikmin on top of it to make it drop some goodies.
Mamuta (even days)
This is a large gray ape-like thing. As bosses go it's actually quite gentle; it doesn't actually hurt your Pikmin but slams them into the ground, turning them back into sprouts. An interesting side effect of this is they are instantly advanced to the flower stage. Mamuta will damage your spacesuit if it hits you though, so try to stay out of range while you throw Pikmin at it. You don't want too many of your Pikmin turned into sprouts since you'll have nothing to fight with, so try to keep them away from its long arms. Reds will be more effective fighters in this battle, but it should be easy enough that you won't actually need them. When the battle is over you'll have a spend a few moments to re-pluck your Pikmin.
Goolix (odd days)
This is a giant amoeba that appears out of nowhere when you enter the area. Leave your Reds and Yellow behind for this since they will just drown in Goolix's watery interior. Point your Blues at the gray, pearly nucleus and they will go to town on it. This works but it will take a while if that's all you do; you can speed things up a bit by throwing Blues at the white nucleus. If you hit it the two nuclei will slam together doing a large amount of damage, though it will stun your Pikmin for a moment. Since Blues are immune to anything the Goolix can do you should be able to get through this battle with no casualties.
Take some Yellows, go inside the cardboard box and get the bomb-rocks there. Take them back to the circular area and knock down the solid wall on the far side. With this done the Yellows are done for the most part and you might as well send 20 home with the large yellow food pellet on the ledge to the left.
Clearing the wall opens up a new area with a pond. Take your Reds and Yellows and start them working on the lattice wall on the left. This will create a shortcut that will save valuable time bringing back the spoils here.
There are new enemies called pearly clamclamps, basically just giant clams with pearls inside. These are actually indestructible but you can knock the pearl out of them, and though this can take a while, the pearl is worth 50 seeds so it can be worth it. There is a clamclamp on land to the right and if you have bombs left over then use them on it to release the pearl in two hits. The other clamclamps are in the water and the one we want is on the left since instead of a pearl it's got the Positron Generator inside. Since it's in the water you must use Blues to attack. Throw about 10 into its mouth, then call them back because the clamclamp will snap shut and munch on any Pikmin still inside. It will take a few tries to finally knock the pearl out; how many tries and how many Pikmin you lose in the process depend on your timing. The middle clamclamp is on a little island and seems be a bit harder to deal with because of this.
When the generator is free, send it and the large blue food pellet home. Send 20 Reds home with the large red food pellet here once they've finished with the wall, and send home any pearls and stray food pellets with the Pikmin that remain. If all goes well then not only will you have the generator by the end of the day, but you will have given a hefty boost to your Pikmin numbers.