Like other games in the franchise, Superdimension Neptune VS Sega Hard Girls has a total of three endings in it and in the case of this game, only one of them is “missable”.
The Good “Normal” Ending
This is the first ending you should come across as you proceed through the game. This ending can be performed at any time by challenging the Time Eater and emerging victorious. You should be capable of doing this around level 50 or so. After completing this ending, you can roll back time again and then work on progressing to the True Ending.
The True Ending
The only real requirement to get this ending is to continue doing missions until you have successfully completed every mission that involves fixing history. If you continue to complete missions you will eventually end up doing this. There are no other requirements to attain this ending. You should be able to accomplish by level 60 or so.
The Bad Ending
In order to attain this ending you must defeat the Time Eater the very first time you encounter him on a playthrough. This is going to require and extremely powerful party to do so, around level 80 for the average party level. In light of this, this is obviously intended to be completed on a New Game +. If you delay as long as possible and ensure you knock out the highest star missions it shouldn’t be too bad.