No offence . . . but I actually really like the finale and thought the writer was brilliant. From my perspective, in the end, Jin Woo died as the user Zinu, but remained as the "Master" of game. Per Se-ju, only Master is given the access to create the "Instance Dungeon" in times of danger to deceive / vanish from enemies. However, based on Se-ju's experience in the Instance Dungeon for the past year, it seems like a third dimension - aside from reality and the virtual world. Therefore, Jin Woo, like Se Ju a year ago, may still be alive and existing in the same time and place but in a different dimension. Different from Se-ju, Jin Woo is not "stuck" in the game and waiting for someone to come rescue him.
With all the tragic events that happened to him, and all the pain that he has to experience in losing and letting go of the ones he loves and trust, Jin Woo "choose" to escape from reality . . . to the third dimension . . . until he is able to overcome his own darkest demons . . . to entrust himself with others and to love again. He trusted and opened his heart to Hee-joo / Emma, but in the end, Emma stabbed and killed him (as Zinu) in the game since she perceived him as a "bug". Also, Jin Woo noticed that those closest to him eventually ends up dead . . . his parents, his best friend (Cha Hyung-seok), his mentor (Professor Cha), his secretary . . . and his doesn't want the love of his life . . . Jung Hee-joo . . . to end up that way . . . he would never forgive himself and would be devastated if she does. Jin Woo has come to the conclusion that he may be a "bug" in reality as well, being the cause of all this tragedy.
For all the things that Jin Woo has been through in the past years, he is having a very hard time distinguishing between reality and non-reality . . . like how Se-ju was having a very hard time telling the difference as to whether the rain and thunder was real or non-real. At the moment, Jin Woo really needs the time to sort things out with himself. As for why he suddenly appears after a year of gone missing, it is because of the launching of the game to the public, and the resulting dangers of its users playing the game in the real world . . . real people were actually getting injured in real life. For this game, it appears that the bug/glitches are created once a real player actually dies while playing the game. Also, it was never noted as to whether or not "Emma" was deleted from the reset, launched version of the game. All in all, the limitation of the game is still a mystery.