The plan

Upon meeting the Doctor at T'zim-Shatons, her former Time Lord companion Roman alluded to "the plan". Assuming that Roman is to be trusted, this is a plot that the Doctor and Roman concocted together, or are at least both involved in, that partially requires the Doctor not to have any memory of it. (The Handheld War)

Background
This incarnation of the Doctor awoke in her TARDIS wearing her predecessor's clothes with a note attached to her that simply says "run". She has no memory of how she regenerated, however her TARDIS had crashed in the early-to-mid 90s requiring her to repair it using the technology of the time. The TARDIS is fitted with a Randomiser, preventing the Doctor from setting a destination and ensuring her arrival points remain randomised.

The purpose of the note and the Randomiser is unknown, though Roman described the current setup as "the running phase." If Roman is telling the truth, he was responsible for writing the note and may also have assisted with installing the Randomiser. The Doctor soon learns who she is running from - the Time Lords, who have dispatched Maxil to track her down.

Unanswered questions
Again, assuming Roman's trustworthiness, several questions remain:
 * Why is the Doctor on the run from the Time Lords?
 * Why does she have no memory of her most recent regeneration?
 * Why would Roman jeopardize the plan by arranging to meet the Doctor to discuss it?
 * Does any of this tie in to Amelia Earhart's temporal amnesia, or Travis and his apparent "death" prior to being plucked from the timeline by Epoch Talent?