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I was playing level 3, got as far as the save spot JUST after you see Mr. Freeze in his cell, and had to quit playing (evidently saving here and assuming I could jump back in to that spot was my mistake). When I restarted the game later that night, I tried replaying level 3 in Story Mode and as soon as I stop Bane's Mole Machine it ends the level and takes me to the Batcave. I can't even choose to move forward with the game either since I can't register completing level 3 in Story Mode.
Now replaying the 3 levels from scratch in a new save file is obviously no big deal, and I'll do that, but:
a) if you choose Save and Quit at a "Save Spot" are you just saving studs and kits you've collected but not your actual progress? And has anyone else NOT been able to replay that level in Story Mode to completion?
b) is there SUPPOSED to be a way to jump back to that point and continue forward in Story Mode?
Heard this exchange at my school: Teacher: "You got a 0 out of 50 on your quiz." Student: "Did that hurt my grade?"
I think you have that backwards since Mr. Freeze's cell is in level 4. Bane's Mole Machine is in level 3.
Not really sure what the deal with the save checkpoints is. I did that on level 5, and turned off the game. Thinking that if you went back to the actual location it would start you at that save spot. It did not, so I played the entire level again, and never saved & quit again (completed each level before quitting the game).
As for your issue, did you try going back to the level 4? Or perhaps (on your old save file if you have it) you can see if it takes you to the saved spot from the Batcomputer?
Or (since there is a known glitch dealing with the Bat-Symbol after level 4) follow the trail of transparent studs (commonly called "ghost studs" since they had that in the LEGO Harry Potter games) to the next level.