One of the things we saw at the end of Agents of SHIELD last season was that Daisy Johnson was off on her own and on the run. So why did this happen? Seems she can't get past the fact that when she was freed and had the opportunity to face Hive / Grant Ward, she was willing to go back to him.
According to Chloe Bennett:
The two people who know she did that are both dead, so no one else knows. There must be a moment coming up in the next season where she reveals that. I think she feels like she can't get close to people because wherever she goes, death follows. That hit home with her, especially this time.
This is likely to bring us a much darker and guilt-riddled Daisy.