I you're returning here after a few days then you will notice that the bulborbs you cleared away previously have now respawned. In fact most of the enemies in the game will respawn if you leave the region alone for a while, so it's better to group your visits unless you want to spend the time to fight the same enemies over again.
There are three more parts to get here.
Sagittarius
Draw about 50 Blues and head southeast to the pond. Cross to a ledge in the southern corner and throw the Pikmin to the ledge where they will find the bridge there and start working on it. It's a long bridge so it's best to leave them to it. Meanwhile draw some Reds and clear the bulborbs from the pond area and the sheargrubs that have appeared near the bridge on the left shore. Start the Reds working on this second bridge so the two bridges will meet on a small peninsula in the middle. When the first bridge is done, go to this peninsula and cross to find the Sagittarius. Collect 20 Blues on the way to send it home, and when the second bridge is done gather the rest of your force to send home spoils. Avoid crossing these bridges with Red or Yellow in tow, especially if you have a large party, since they are liable to get on the wrong side of the railing and fall into the water.
Radiation Canopy
Go northwest from the ship with about 50 blues, turn right at the passage where the Nova Blaster was located, and put them to work on the lattice wall in the puddle on the left. While they're working, get about 50 Reds and take them northwest from the ship, but this time continue northwest, clearing any bulborbs on the way. Throw the Red onto the ledge to the north. When the Blues have finished, which ideally will be a just about the time you've thrown the last Red to the ledge, collect them, continue through to a small area where there is another lattice wall. Put the Blues to work on it and grab the Reds, which should be waiting nearby, to work on it as well. With nearly 100 working it shouldn't take too long to finish.
When the wall is down, gather your Pikmin and confront the enemy lurking beyond, the armoured cannon beetle. It really resembles a spider more than anything else, though it only has four legs. It attacks by taking a huge breath, then blowing out a cannon ball which will wipe out anything in its path. It lives up to the armored part of its name as well since nothing the Pikmin can do will penetrate its thick, iron-like shell. Defeating it isn't that hard once you discover the trick though. Wait until is about to inhale, then start throwing Pikmin in its face so that one will get sucked in a clog up its breathing hole. This fouls up its ventilation mechanism somehow because it will then open its wings to cool off, exposing its vulnerable inner skin. Quickly maneuver around behind it and start throwing Pikmin at it like mad. After a few seconds the beetle will recover and shake off the Pikmin on its back, so gather them up and start the process over. Above all, keep your Pikmin away from its front unless your confident you can get a Pikmin into its mouth. When the beast is down, send its body back since it's worth a good number of seeds, and assuming you haven't taken too many casualties you should have enough left over to send back the Radiation Canopy which is waiting in the corner.