Doctor Who: Every Doctor's Darkest Moment

There's a lot of darkness hiding under the shabby exterior of the Second Doctor. His most notable shady moment comes in The Evil of the Daleks, when he manipulates his companion Jamie McCrimmon. 

Jamie is being used by the Daleks and the Doctor to test the "human factor", something that the sinister salt shakers want to understand to improve their military strategy. 

It's later revealed to be part of a larger plan by the Doctor to defeat the Daleks once and for all, by "infecting" them with the human traits of cooperation and compassion.

Jamie chastises the Doctor for his manipulation, and it stings to see this particular TARDIS team briefly at odds with each other. However, it's another strong example of how the Doctor's big picture thinking doesn't always guarantee the safety of his companions.