In The Garden, Hope explains part of her life story to Gabriel and Echo as well as the fact that she had made a deal with the Disciples' leader Anders -- the "he" that she had previously mentioned -- wherein Hope would help to capture Octavia by tagging her so that she would be sent back through the Anomaly in exchange for Diyoza's life.
In Anaconda, Anders brings Bill Cadogan to meet with Clarke's group and remains outside with the rest of the Disciples on his request. When Gabriel opens the door again, Anders sends in Clarke's friends upon her request.
In A Little Sacrifice, Anders protests Cadogan's orders to leave Clarke and her friends alone, but ultimately complies. He later interrupts Cadogan's dinner with Gabriel Santiago to warn him of a problem, disarming Gabriel before allowing him to go back to the Stone room.
As Clarke and her friends talk Echo down from unleashing Gen-9 on Bardo, Anders enters, furious at their actions, the deaths of three of his people, the torture of Levitt and attempting to commit genocide. Diyoza hands over the Gen-9, offering to call it even, but Anders is disgusted by them for being "nothing but primal beasts" since they were raised in the wild who are utterly enthralled in their feelings and prioritizing the want of self over the needs of everyone. Though Miller threatens Anders, Diyoza recognizes that Anders is not alone and four Disciples decloak behind him.
Diyoza points out that its a bad idea to fire lasers in a room with a WMD and suggests getting back to the Shepherd's mercy. Anders offers to send Echo to Penance for 20 years, but promises that she will be back before they know it as long as the code has been entered by then to begin the last war or Echo will die there. Stating that she has a better idea, that Anders dies there, Hope slits Anders' throat, causing him to drop the Gen-9 as he desperately grabs at the wound. As Anders falls to the ground holding his wound, Hope attempts to release the bioweapon, only to be stopped by Diyoza. However, Gen-9 is released in the room, crystalizing Diyoza and Anders and everything else within.
In Etherea, it is mentioned that no one has been punished for Anders' death due to Clarke's group controlling the Key and that they have even been given Anders' and Cadogan's quarters. Going through the memory of a Disciple that has PTSD from the explosion that apparently killed Bellamy, Levitt discovers that he actually survived and was instead blown through the Anomaly which Anders had opened to Etherea instead of Sanctum as Octavia had requested.
In The Stranger, Bellamy offers his condolences to Cadogan for the loss of Anders, assuming that they were close. Cadogan states that he actually only met Anders twice with each First Disciple usually awakening him every 20 years to state that there has been no progress with the last war. Anders was the only one to wake him twice, the second time because they had found the Key. Cadogan agrees that "comparatively speaking", they were close, but recognizes that Bellamy was merely testing him with the question.