Many of you may have played, or heard of Cave Story, if not, Google or Bing it and get out from under that rock. I have a theory about the past leading up to the events in Cave Story that explains why you are alone and why that gunsmith is in the cave, the one you get the polar star from.
After Ballos creates the demon crown and places curses on Misery and balrog, (both may be related to him, and I think Jenka is his sister), an explorer comes to the island to study the local flora and fauna. Finding the crown, he decides to wear it as a helmet. The crown makes the explorer go insain and he decides to conquer the world below. After learning about the red flowers, he feeds them to the mimigas as they are released from the island. The resulting chaos forces a response from below. Because humans are too weak against the crazed mimigas, robots are built and sent to the island to eradicate the mimigas. The gunsmith is sent with them to repair and arm the robots. After a bloody battle, the gunsmith is disgusted that innocent mimigas are being used and killed. He starts reprogramming the robots to take each other out, until Quote is the only one getting repairs and guns. Because Curly is a command unit (gives commands to other robots), she has greater intellect and empathy for the mimigas and disappears. Quote is given orders by the gunsmith to defeat the person wearing the crown, and after the gunsmith removes Quote's battery so his capacitors discharge and resets him. While the gunsmith is working on the polar star, the Sakamotos arrive and stay away from the mimigas. After the doctor finds the demon crown, he has misery turn sue into a mimiga and find the red flowers. As the mimigas are being rounded up, the gunsmith takes a walk to his secret stash of robot parts to finish the polar star, along the way, re replaces Quote's battery so he'll start rebooting. Quote reboots faster than the gunsmith anticipates, and gets the unfinished gun, thus starting the game.