The humans started using the energy of the planet as if it was the new free energy, and the planet was dying. The dragons and a goddess in disguise were against that. That goddess is Kuro's first love. She was originally one of the creatures created by the planets, with a robot-like mind, but she got bugged and started liking the humans. She is the third party that stood against the dragons, even if the humans were the ones at fault. After the other dragons leave, she decide to sacrifice herself to give her energy to the planet to save it, with the help of Potimas, the now leader of the elves (Not sure, but the elves should all be his descendents). He actually planned on stealing the energy obtained by killing the goddess and keep it for himself instead of giving it to the planet. In the meantime Kuro goes to ask for help to D, who is a big-shot evil goddess, who stops the goddess from suicide, create that huge System to restore the energy of the planet by enslaving all its inhabitant, by using the goddess as its driving force. The System worked for a while and the planet was being restored. It's not shown in the story yet, but the other half of the planet is a huge dead desert. The original idea was for the goddess to survive. But a previews hero and daemon king manage to waste the planet's energy to try and kill D, which is obviously a failure as D is way too OP. (I think it was Kuro who made them do this, or was somewhat involved. Not sure) This is the incident that causes the class to be transported on that planet, and practically seals the goddess' life as too much energy was wasted. Right now the system can't even gather enough energy to restore itself, let alone balance the waste continuously made by the elves. If only Kuro acted against them instead of being a wimp.
The MC was taken in as a protegee of D, but (I think) her current task is to help the demon lord, who was created by Potimas's failed experiments on humans before the system. The demon lord loved the goddess and wanted to save her against her will, instead of having her and kuro die to save the planet. MC plans on destroying the system, kill Potimas, and wave a huge war to kill as many people as possible, to free the energy for the planet. The system works by forcing people to reincarnate on the same planet over and over again, train the skills and fight, so that they create a surplus of energy when they advance their skills. Energy that is collected by the system on their death to help the planet. Also, those that don't get killed in the war probably will have their soul destroyed as it's too deteriorated to sustain the impact. I don't remember exactly why tho.
Some things I'm not sure, but the rest should have happened like this in the WN. The manga is based on the LN, so I don't know how much will actually happen. Lastly, the one who saved the teacher from certain death after she tried to remove the skills from a student is the MC after she becomes a goddess and administrator of the system. Kuro, D and the goddess are the other admins.