In the episode, the alien time traveller the Doctor (Peter Capaldi) disappears and gives a confession dial—his version of a last will and testament—to his former childhood friend Missy (Michelle Gomez).

The Doctor feels shame for having abandoned Davros as a boy, and agrees to be taken away; Missy and Clara persuade Sarff to take them as well.

The Doctor attempts to plead for their lives, but Davros says he has no control over the Daleks, and Missy, Clara, and the TARDIS are seemingly destroyed.

[11][13] The Sisterhood of Karn, already seen in the 2013 teaser "The Night of the Doctor", originally appeared in the 1976 serial The Brain of Morbius.

[13][14] UNIT seeks the Doctor using a computer algorithm, plotting on a map the locations of various crises at which he has been rumoured to have appeared.

These correspond with locales for many of the Doctor's past adventures: San Martino (The Masque of Mandragora);[10] New York City (The Chase, "Daleks in Manhattan"/"Evolution of the Daleks", and "The Angels Take Manhattan") and three possible appearances in Atlantis (The Time Monster, The Underwater Menace, and The Dæmons).

[10] Davros plays excerpts from his prior conversations with the Doctor's earlier incarnations, ranging from Genesis of the Daleks to "The Stolen Earth".

"[11] Several different designs of the Daleks from across the series' history reappear in the episode, alongside their creator, Davros, and their home planet, Skaro.

[11] Clara, upon deducing the Doctor's location and intent, says "Do not go gentle into that good night", the first line of the titular poem by Dylan Thomas.

[10] When the Doctor spies Clara and Missy, he plays the opening notes to Roy Orbison's "Oh, Pretty Woman".

[16] The Doctor's playing electric guitar and teaching medieval people the term "dude" echoes the movies Bill & Ted's Excellent Adventure and Bill & Ted's Bogus Journey, films featuring two rocker teens who travel back in time – in a telephone call box – and teach historical figures their customs.

[16] Actor Peter Capaldi plays the guitar himself and was part of a punk rock band called The Dreamboys in the early 1980s alongside Craig Ferguson.

Clare Higgins played Ohila of the Sisterhood of Karn in the mini-episode "The Night of the Doctor", which was part of the 50th Anniversary specials in 2013, and again in the season finale "Hell Bent".

Jami Reid-Quarrell made a subsequent appearance as "The Veil" in "Heaven Sent", the penultimate episode of Series 9.

The site's consensus reads, "In 'The Magician's Apprentice', Peter Capaldi and the writers settle into an emotionally engaging tone while raising the stakes for the Twelfth Doctor".

[11] Nick Setchfield of SFX also gave the episode five stars, claiming it was "full of wit and menace" and "unafraid to take on the show's museum piece classics".

[38] However, Benji Wilson in The Daily Telegraph gave it 3/5, saying that the "jury is still out" and questioning whether "seemingly catastrophic events" can be very thrilling in the Doctor Who universe which "keeps reminding you you're not supposed to take it seriously".