Explanation: Various Adventure Items

These gateways are made from parts of the emerald within Frost, which she agreed to severe from her soul for the sake of letting other Jammers help in the war to come. The three orbs hold spirits, which power the entire portal. Greely checks them daily to make sure none of the portals malfunction and lead you outside of the base camp. Before you free the area you explored of the phantoms' grip, though, they cannot draw on enough power to transport you away. Teleporting works, but it undoes some of your efforts because of the mana it consumes.
The treasure chests are things Mira dropped in Bunny Hollow a long time ago for a scavenger hunt, then forgot to host it and left the chests full of money to rust. However, when Lisa was exploring Bunny Hollow and allying with the inhabitants within it, she found these chests and restored them to their former glory in case it was needed later.
As for the Arctic Wolf sigil, Olivia left it there as a prize for her brethren to use to get to the Crystal Cavern, in which they find a random prize and a whole bunch of fluorite jewels. Zios's emblem is on it to power it, as all of his symbols are filled with Father Sky's power. Blue light erupts inside it due to it taking some of the mana of the unlocker.
For the checkpoints, they are creations of the elite priests of Zios, and revive tired Jammers from their ailments to full vigor. Most of them were placed around Jamaa to help the elderly and sick recover, but when the Phantoms invaded most were destroyed in the utter chaos. Lisa, however, salvaged some and placed them around the areas phantoms had captured for explorers and heroes alike to use to their advantage. When they were put into a sleep by the phantoms and ready to be dark-shellified, these yanked them away to safety.
For those plants, Cosmo created them to devour phantoms on contact so that they didn't have to fight them all of the time. However, because it takes a lot of effort to divert the energies inside a phantom to make it into more time energies, they could only devour one phantom per day.
Phantoms cannot see you in tall grass because of their one eye. They have poor eyesight, and so cannot see very well. However, when they find you, the weak and powerless are forced to flee!
The Phantoms poisoned the river by summoning pipes from the sewers, therefore making a dark layer of poisonous ice over the water that infected any plant material it touched. However, by corking these pipes and making them blow up from pressure, the spell breaks and everything but the plants returns to normal.