Rose Tyler

Rose Tyler gets +1/+1 for each time counter on it.
Bad Wolf — Whenever Rose Tyler attacks, put a time counter on it for each suspended card you own and each other permanent you control with a time counter on it.
Doctor's companion (You can have two commanders if the other is the Doctor.)

Nyssa of Traken

You have no maximum hand size.
Sonic Booster — Whenever Nyssa of Traken attacks, sacrifice X artifacts. When you sacrifice one or more artifacts this way, tap up to X target creatures and you draw X cards.
Doctor's companion (You can have two commanders if the other is the Doctor.)

Amy Pond

Partner with Rory Williams (When this creature enters the battlefield, target player may put Rory into their hand from their library, then shuffle.)
Whenever Amy Pond deals combat damage to a player, choose a suspended card you own and remove that many time counters from it.
Doctor's companion (You can have two commanders if the other is the Doctor.)

K-9, Mark I

Negative — As long as K-9, Mark I is untapped, other legendary creatures you control have ward {1}.
Affirmative — {1}{U}, {T}: Target legendary creature can't be blocked this turn.
Doctor's companion (You can have two commanders if the other is the Doctor.)

Bill Potts

Whenever you cast an instant or sorcery spell that targets only Bill Potts or activate an ability that targets only Bill Potts, copy that spell or ability. You may choose new targets for the copy. This ability triggers only once each turn.
Doctor's companion (You can have two commanders if the other is the Doctor.)

The Fugitive Doctor

When The Fugitive Doctor enters the battlefield, investigate.
Whenever The Fugitive Doctor attacks, you may sacrifice a Clue. When you do, target instant or sorcery card in your graveyard gains flashback {2}{R}{G} until end of turn. (You may cast that card from your graveyard for its flashback cost. Then exile it.)

The Third Doctor

Trample
The Third Doctor gets +1/+1 for each noncreature token you control.
When The Third Doctor enters the battlefield, create your choice of a Clue token, a Food token, or a Treasure token.

The Fifth Doctor

Peaceful Coexistence — At the beginning of your end step, put a +1/+1 counter on each creature you control that didn't attack or enter the battlefield this turn. Untap those creatures.

Sarah Jane Smith

Whenever you cast a historic spell, investigate. This ability triggers only once each turn. (Artifacts, legendaries, and Sagas are historic. To investigate, create a Clue token. It's an artifact with "{2}, Sacrifice this artifact: Draw a card.")
Doctor's companion (You can have two commanders if the other is the Doctor.)

Clara Oswald

Impossible Girl — If Clara Oswald is your commander, choose a color before the game begins. Clara Oswald is the chosen color.
If a triggered ability of a Doctor you control triggers, that ability triggers an additional time.
Doctor's companion (You can have two commanders if the other is the Doctor.)

Tegan Jovanka

Brave Heart — Whenever you attack, target attacking historic creature gets +1/+1 and gains indestructible until end of turn. (Artifacts, legendaries, and Sagas are historic.)
Doctor's companion (You can have two commanders if the other is the Doctor.)

The Tenth Doctor

Allons-y! — Whenever you attack, exile cards from the top of your library until you exile a nonland card. Put three time counters on it. If it doesn't have suspend, it gains suspend.
Timey-Wimey — {7}: Time travel three times. Activate only as a sorcery. (For each suspended card you own and each permanent you control with a time counter on it, you may add or remove a time counter. Then do it two more times.)

Susan Foreman

If you would planeswalk, instead look at the top two cards of your planar deck, put one on the bottom of your planar deck and the other on top, then planeswalk.
{T}: Add {G}.
Doctor's companion (You can have two commanders if the other is the Doctor.)

Dan Lewis

Noncreature, non-Equipment artifacts you control are Equipment in addition to their other types and have "Equipped creature gets +1/+0" and equip {1}.
Doctor's companion (You can have two commanders if the other is the Doctor.)

Jamie McCrimmon

Trample
Whenever you cast a historic spell, Jamie McCrimmon gets +X/+X until end of turn, where X is that spell's mana value. (Artifacts, legendaries, and Sagas are historic.)
Doctor's companion (You can have two commanders if the other is the Doctor.)

Vislor Turlough

Deal with the Black Guardian — When Vislor Turlough enters the battlefield, you may have an opponent gain control of it. If you do, it's goaded for as long as they control it.
At the beginning of your end step, draw a card, then you lose life equal to the number of cards in your hand.
Doctor's companion (You can have two commanders if the other is the Doctor.)

Martha Jones

Woman Who Walked the Earth — When Martha Jones enters the battlefield, investigate. (Create a Clue token. It's an artifact with "{2}, Sacrifice this artifact: Draw a card.")
Whenever you sacrifice a Clue, Martha Jones and up to one other target creature can't be blocked this turn.
Doctor's companion (You can have two commanders if the other is the Doctor.)

Adric, Mathematical Genius

{2}{U}, {T}: Copy target activated or triggered ability you control. You may choose new targets for the copy.
Ultimate Sacrifice — {1}{U}, Sacrifice Adric: Counter target activated or triggered ability.
Doctor's companion (You can have two commanders if the other is the Doctor.)

The Ninth Doctor

Haste
Into the TARDIS — Whenever The Ninth Doctor becomes untapped during your untap step, you get an additional upkeep step after this step.

Romana II

Vigilance
{1}, {T}: Create a tapped token that's a copy of target token that entered the battlefield this turn.
Doctor's companion (You can have two commanders if the other is the Doctor.)