To be fair on this point, think basically everyone knew she was going to somehow show up for the final confrontation somehow. Although her getting "rescued" so early in the season and having her trail around like a Prophet of Doom was some kind of choice...but it does lend itself to the only real plot/character point that makes sense. Eleven dealing with the idea that portions of the military forever coming after her to continue experiments to turn kids into weapons with some version of her superpowers.
Of course, given how easily the former drunk police chief and Nancy "I'm Suddenly the Female Rambo" Wheeler mow through military red shirts, don't know why they even worry about it.