Maybe there will be a hint to the manner of Clara's departure in episode 2 "The Witch's Familiar"
Last year Moffett totally ignored the supposed relationship between Missy and Clara (from Flat Line "My Clara. I
have chosen well."). it looks likely that having re-secured the services of Jenna and Michelle, he's going to correct that omission this year.
We know
Missy was the woman in the shop who gave Clara the Doctor's telephone number and brought the two of them together.
Missy kept them together after the Doctor's regeneration by placing the announcement in the newspaper
Possible scenario
Missy give the Doctor the technology to bring back Danny Pink from the dead in Death In Heaven but she already knew that Danny had a massive guilt complex over the little boy he killed when he was a soldier, so she knew he would sacrifice his chance to get home for the boy and thus Clara and the Doctor would continue to travel together. But the Doctor and Clara lied to each other and went their separate ways.
So Missy sent in the dream crabs to bring them together in Last Christmas. Success!
But then in series 9 episode 1 something happens to split up the Doctor and Clara either by accident or design.
So Missy decides "If you want a job done properly, do it yourself".
We know
Missy meets Clara and declares "I need your help" and "The Doctor is in trouble"
Possible scenario
This is clearly a trade-off "You help me, Clara, and I'll help you find the Doctor again". There can be no other reason for Clara to agree to help Missy.
Casting suggests The Sisterhood Of Karn may be back in the opening two-part story. Maybe the Sisterhood have possession of Missy's TARDIS. "You get my TARDIS back from the Sisterhood, Clara, and I'll use it to help you find the Doctor.
But at some point Clara annoys Missy so Missy angrily (and hopefully scarily) blurts out the real reason why Missy goes to so much effort to get the Doctor and Clara together.
Maybe it's something as simple as the Doctor caring so much for his Impossible Girl that he breaks the rules for her:
He entered his own grave at Trenzalore to save his Impossible Girl (that must be against the rules, surely.)
He tried to bring Danny Pink back from the dead (that's
definitely against the rules) and he did so despite Clara's betrayal (which shows how much he cares for her.)
He was going to kill Missy to stop Clara from killing her and becoming a killer (thus reducing himself to Missy's level - something Missy enjoys)
He used technology provided by Missy to try to bring Danny back from the dead (thus reducing himself to Missy's level)
"If you continue to travel with the Doctor, he's going to end up doing something
SO BAD to save his Impossible Girl".
Missy then wipes Clara's memory of this "conversation" and orchestrates a reunion between the two, either by Clara saving the Doctor from danger or the Doctor saving Clara from danger (preferred option

)
then in the series finale the Doctor is going to do something SO BAD to save Clara that she sacrifices herself to stop him doing something SO BAD.
Or - alternatively
The Doctor
nearly does something
SO BAD but in the end finds a NOT BAD way to save Clara, they both realise it's dangerous for her to continue to travel with him, so he takes her home to Earth and they say a final emotional goodbye. (the cop-out ending.

) (Preferred option.


)