Been trying since that stupid "Divisive Mind" bounty showed up. If you start from the Cyclops checkpoint in The Black Garden mission, the Divisive Mind will NOT spawn. So naturally, you have to go through this entire mission to get the proper reset to spawn the Divisive Mind. As far as I know, he will only spawn if you start it from the beginning.
Now to my point. When you hover above the Black Garden mission with your cursor and you have a checkpoint in that mission on any difficulty, you'll see an option that says "X (or Square) Restart", basically telling me that there is a way I can restart my checkpoints and start from the beginning, right?
Wrong. When you press this, it will take you to your ship screen to select a level. Select your desired level and voila, you're still at the checkpoint.
Please fix this. It's hella annoying.
Edit:
Thanks for the help guys. Didn't realize you could press X when setting a diffculty.
As for all you "HAHAHA UR AH CRISSMASS NUUB ARNT U" no. I'm not. Been playing since Beta. So -blam!- off.
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I had the same problem so I just beat the whole thing and started over