The season continued to star William Hartnell as the first incarnation of the Doctor, an alien who travels through time and space in his TARDIS, which appears to be a British police box on the outside.

Carole Ann Ford continued her role as the Doctor's granddaughter Susan Foreman, who acts as his companion alongside her schoolteachers Ian Chesterton and Barbara Wright, portrayed by William Russell and Jacqueline Hill, respectively.

Ford departed the series at the conclusion of the season's second serial, The Dalek Invasion of Earth, replaced by Maureen O'Brien as Vicki in the following story, The Rescue.

[19] In August 1964, Lambert cast Pamela Franklin as Jenny (originally known as Saida) in The Dalek Invasion of Earth to replace Ford as Susan;[20] some days later, the character was rewritten to become a more minor role, with the new companion to be introduced in the following serial.

Their departure was announced on 1 April 1965; Russell explained that the creativity had gone and he wanted to reenter comedy and theatre performances, and Hill said that "It has been great fun, but you can't go on forever".

[12] Lambert worked with the story editors to keep the show feeling fresh, attempting new avenues such as the overt humour of The Romans and The Chase, the "downright weirdness" of The Web Planet, and the pseudo-historical content of The Time Meddler.

[40] The concept of The Giants was given to writer Robert Gould in mid-1963 to develop as the four-part fourth serial of the first season, but it was dropped by January 1964 due to scripting difficulties.

[42] The main narrative was inspired by Rachel Carson's 1962 environmental science book Silent Spring, the first major documentation on human impact on the environment.

[47] He rejected at least two proposals: The Hidden Planet by Malcolm Hulke due to necessary rewrites after Susan's departure, and a lack of science-fiction monsters;[47] and The Slide by Victor Pemberton as he felt it was a messy blend of the show's science fiction stories to date and disliked the dialogue.

[51] For The Crusade—intended to balance the show's science fiction stories[37]—Whitaker was inspired by the Third Crusade; he found that some of the historical figures—namely King Richard and his sister Joan, whose affectionate relationship he considered "almost incestuous in its intensity"—were effective material for a character drama.

[70] The show's regular cast—Hartnell, Russell, Hill, and Ford—filmed the sequences in which they appeared alongside giant props; the effect was achieved by recording the actors through glass and reflecting the object onto a half-silvered mirror.

[66] Due to director Mervyn Pinfield's other commitments, the fourth and final episode was directed by Douglas Camfield, who had worked as a production assistant to Waris Hussein during the show's first season.

[75] The Dalek Invasion of Earth, directed by Richard Martin, was the first major location shoot for Doctor Who, with 35 mm filming in central London at Trafalgar Square, the statue of the Duke of Cambridge in Whitehall, Westminster Bridge, and the Royal Albert Hall in August 1964.

[85] Directed by Christopher Barry, it was recorded on 4 and 11 December 1964 at Riverside Studios;[86] there was a happy atmosphere among the cast, including a picnic in Hartnell's dressing room on the first week.

[89] Martin wanted to use a greased neutral-density filter on shots of Vortis to capture its thin atmosphere, but found that the optical glass was too expensive, opting for a cheaper alternative;[90] two special lenses were fitted, both of which broke at some point during production.

Hartnell found the change unsettling and threw fake tantrums to scare the production team to obey him; he later admitted to other cast members that he was only joking.

[103] In September 1964, the BBC announced that Doctor Who would return for its second season in October, emphasising that it was one of its core pieces of content alongside coverage of the general election.

[107] A special trailer for The Web Planet, filmed on 4 February 1965, features the Zarbi arriving at the BBC Television Centre before being shown to their dressing rooms.

The show received extensive publicity during the broadcast of The Time Meddler due to the release of Dr. Who and the Daleks; on 28 July, Lambert was interviewed by Denis Tuohy on Late Night Line-Up, and the Daily Mirror published a story about Hartnell's life and career.

[113] Planet of Giants was transmitted on BBC1 in three weekly parts from 31 October to 14 November 1964, at 5:15 p.m.[114] The BBC Film and Videotape Library did not select the serial for preservation, and the original tapes were wiped in the late 1960s.

[127] Viewership numbers for The Chase were considered extremely positive, though the early summer months meant that it failed to gain the high audience figures for serials like The Dalek Invasion of Earth and The Web Planet.

[179] The Web Planet received mixed reviews; the first episode was criticised by Peter Black of the Daily Mail, who described the main characters as "the dullest quartet in fiction".

[180] Patrick Skene Catling of Punch wrote that the serial was guilty of "ludicrous bathos",[180] and Bill Edmund of The Stage and Television Today described the lighting effects as "pointless and annoying".

[180] The Crusade was well-received; Bill Edmund of Television Today directed praise at Glover's performance and Whitaker's writing, declaring "the dialogue and the story ... one of the best we have had in this series".

[123] Conversely, Television Mail wrote that "the appallingly flat dialogue of Dr Who could hardly be heard ... above the creaking of the plot", noting that the show should only be viewed "by people who have a profound contempt for children".

[126] The Space Museum received a mixed response; the Times Educational Supplement described the serial as "enormously contrived", adding that the series "has run out of imagination".

[190][191] Marjorie Norris of Television Today described the final episode as "far and away the most dramatically successful" in the show's history, praising the battle between the Daleks and Mechonoids, the music and design, and the performances of Hartnell and Purves.

[181] Conversely, Philip Purser of the Sunday Telegraph described the show as "a ramshackle old serial these days" and noted that the Daleks were "fast losing their ancient menace".

In The Television Companion (1998), David J. Howe and Stephen James Walker found the plot of Planet of Giants to be "one of the weakest" in the series so far; they praised Hill's performance, and enjoyed Hartnell and Russell, though noted that Ford was "rather less impressive".

[205] Some reviewers found The Chase's final episode to be its strongest, largely due to the battle between the Daleks and the Mechonoids and departure of Ian and Barbara;[206][207][208] Cornell, Day, and Topping described the serial as "one of the most bizarre", consisting of "unconnected set pieces with only the barest remnant of a plot".