The First Doctor grew progressively weaker while battling the Cybermen during the events of The Tenth Planet and eventually collapsed, seemingly from old age. His body renewed itself and transformed into the Second Doctor.
Initially, the relationship between the Second Doctor and his predecessor was unclear. In his first story, the Second Doctor referred to his predecessor in the third person as if he were a completely different person. His companions Ben and Polly are at first unsure how to treat him and it is only when a Dalek recognises him that they accept that he's the Doctor.
In the second story, The Highlanders, Jamie McCrimmon joined the TARDIS crew, and remained with the Second Doctor for the rest of his travels. Ben and Polly left together when the TARDIS landed at Gatwick Airport on the same day they originally left with the First Doctor. The Doctor and Jamie then became involved in a plot by the Daleks to gain both the "Human and Dalek Factors", which led to them meeting Victoria Waterfield in the 19th century. The Doctor used the situation to engineer a Dalek civil war that seemingly destroyed the Daleks forever. However, Victoria's father was among the casualties. Now an orphan, Victoria chose to accompany the Doctor and Jamie on their travels. Although she felt great affection for the Doctor and Jamie, she was never able to completely come to terms with life in the TARDIS and the constant danger that resulted. She eventually chose to leave after the events of Fury from the Deep. The Doctor was then joined by Zoe Heriot, an extremely intelligent (if overly dependent on logic) woman from the 21st century, who helped defeat the Cybermen attack on a space station known as the Wheel. She then stowed away in the TARDIS and, despite the Doctor's warnings about what she might encounter, chose to remain.
During his second incarnation, the Doctor confronted familiar foes such as the Daleks and the Cybermen, as well as new enemies such as the Great Intelligence and the Ice Warriors. It was during this time that he first met Alistair Gordon Lethbridge-Stewart, in the tunnels of the London Underground. Following the defeat of the Great Intelligence, Lethbridge-Stewart was promoted to Brigadier and became the leader of the British contingent of UNIT, a military organisation tasked to investigate and defend the world from extraterrestrial threats. The Doctor reteamed with him to defeat an invasion of Cybermen in league with industrialist Tobias Vaughan.
The Second Doctor's time came to an end when the TARDIS landed in the middle of a warzone, created by a race of alien warlords who progressively kidnapped and brainwashed humans into becoming soldiers for them. Although the Doctor was able to defeat their plan, he realised he would be unable to return the human subjects to their various original points in Earth's history. He therefore contacted the Time Lords, sacrificing his own freedom in the process. He was then put on trial by the Time Lords, for breaking their laws of non-interference. Despite the Doctor's argument that the Time Lords should use their great powers to help others, he was sentenced to exile on 20th century Earth, the Time Lords forcing his regeneration into the Third Doctor in the process. Jamie and Zoe were returned to their own time, with their memories of all but their first encounter with the Doctor wiped and the secret of the TARDIS was also taken from the Doctor