The Hybrid's Choice starts of the final box set of the War Doctor Begins with the continuation of the main story arc of the range, the downfall of the War Doctor's (to date) only companion Case. A berzerker class cyborg kidnapped and augmented by the Daleks but somehow managed to break her programming and briefly side with the Time Lords. But after growing frustrated with being looked at as a monster and seeing the Doctor as someone who was trying to manipulate her, Case ended up leaving with the Dalek Time Strategist. This leads into The Hybrid's Choice written by Case's voice actress herself Ajjaz Awad-Ibrahim. The main focus is primarily on Case and how the Daleks seem to be gradually winning her over to their side, particularly with her own Dalek therapist who's given some very unusual and slightly unnerving lines for a Dalek, I never thought I'd hear the word "cake" come up in Dalek dialogue but there we go. As she gets more comfortable being on the side of the Daleks it isn't long before they unleash her on the Time Lords and we see just how dangerous Case can be when living up to her full potential. But despite her willingness to fight for the Daleks, she still grapples with her inner conflict and her lack of knowledge at her true identity.

The War Doctor plays his part by initially mourning what he believed was her death only to realise not only is she still alive but that she has now fully turned against him, and so he tries one final attempt to rescue her only to be rejected. One of the things that works thematically about the War Doctor Begins is that throughout the range the War Doctor still tries to hang on to his old principles, when the series began he started off as something of an enthusiastic warrior eager to get started, now we start to see him beginning to tire and gradually give up on what's left of his Doctor persona as shown in the final scene, with him even joining in on the assault on the Daleks. It's not a perfect story, one of my issues with Case in general is sometimes her lines can be a bit corny and her conflict in choosing between the Doctor and Daleks gets a bit bungled when the flashback sequence openly shows her that the Daleks invaded and destroyed her world. But it's still a great opener.