The War Doctor

Whenever one or more other permanents phase out and whenever one or more other cards are put into exile from anywhere, put a time counter on The War Doctor.
Whenever The War Doctor attacks, it deals damage equal to the number of time counters on it to any target. If a creature dealt damage this way would die this turn, exile it instead.

Kate Stewart

Whenever you put one or more time counters on a permanent you control, create a 1/1 white Soldier creature token.
Whenever Kate Stewart attacks, you may pay {8}. If you do, attacking creatures get +X/+X until end of turn, where X is the number of time counters among permanents you control.

Chronozoa

Flying
Vanishing 3 (This creature enters with three time counters on it. At the beginning of your upkeep, remove a time counter from it. When the last is removed, sacrifice it.)
When this creature dies, if it had no time counters on it, create two tokens that are copies of it.

Sinister Concierge

When this creature dies, you may exile it and put three time counters on it. If you do, exile up to one target creature and put three time counters on it. Each card exiled this way that doesn't have suspend gains suspend. (For each card with suspend, its owner removes a time counter from it at the beginning of their upkeep. When the last is removed, they may cast it without paying its mana cost. Those creature spells have haste.)

Run for Your Life

One or two target creatures each gain haste until end of turn. They can't be blocked this turn except by creatures with haste.
Escape—{2}{U}{R}, Exile four other cards from your graveyard. (You may cast this card from your graveyard for its escape cost.)

Regenerations Restored

Vanishing 12 (This enchantment enters with twelve time counters on it. At the beginning of your upkeep, remove a time counter from it. When the last is removed, sacrifice it.)
Whenever one or more time counters are removed from this enchantment, scry 1 and you gain 1 life. Then if this enchantment has no time counters on it, exile it. When you do, take an extra turn after this one.

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.)

Dinosaurs on a Spaceship

Vigilance, trample
Other Dinosaurs you control get +1/+1 and have vigilance and trample.
Suspend 4—{3}{R}{W}
Whenever a time counter is removed from this card while it's exiled, create a 2/2 red and white Dinosaur creature token with flying and haste.

Yasmin Khan

{T}: Exile the top card of your library. Until your next end step, you may play it.
Doctor's companion (You can have two commanders if the other is the Doctor.)

Lost Auramancers

Vanishing 3 (This creature enters with three time counters on it. At the beginning of your upkeep, remove a time counter from it. When the last is removed, sacrifice it.)
When this creature dies, if it had no time counters on it, you may search your library for an enchantment card, put it onto the battlefield, then shuffle.

The Parting of the Ways

(As this Saga enters and after your draw step, add a lore counter. Sacrifice after III.)
I — Exile the top five cards of your library. For each nonland card exiled this way, put a number of time counters on that card equal to its mana value. If it doesn't have suspend, it gains suspend.
II — Time travel, then time travel.
III — For each opponent, destroy up to one target artifact that player controls.

Graham O'Brien

Paradox — Whenever you cast a spell from anywhere other than your hand, create a Food token. (It's an artifact with "{2}, {T}, Sacrifice this token: You gain 3 life.")
Doctor's companion (You can have two commanders if the other is the Doctor.)

Amy Pond

Partner with Rory Williams (When this creature enters, 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.)

Time Beetle

Skulk (This creature can't be blocked by creatures with greater power.)
Parallel Universe — Whenever this creature deals combat damage to a player, time travel. (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.)

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.)

Nyssa of Traken

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

The Twelfth Doctor

The first spell you cast from anywhere other than your hand each turn has demonstrate. (When you cast that spell, you may copy it. If you do, choose an opponent to also copy it. A copy of a permanent spell becomes a token.)
Whenever you copy a spell, put a +1/+1 counter on The Twelfth Doctor.

An Unearthly Child

(As this Saga enters and after your draw step, add a lore counter. Sacrifice after III.)
I, II, III — Reveal cards from the top of your library until you reveal a Doctor card, a card with doctor's companion, or a Vehicle card. Put that card into your hand and the rest on the bottom of your library in a random order.

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.)

TARDIS

Flying
Whenever this Vehicle attacks, if you control a Time Lord, the next spell you cast this turn has cascade and you may planeswalk.
Crew 2 (Tap any number of creatures you control with total power 2 or more: This Vehicle becomes an artifact creature until end of turn.)

The Eleventh Doctor

I. AM. TALKING! — Whenever The Eleventh Doctor deals combat damage to a player, you may exile a card from your hand with a number of time counters on it equal to its mana value. If it doesn't have suspend, it gains suspend.
{2}: Target creature with power 3 or less can't be blocked this turn.

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.)

K-9, Mark I

Negative — As long as K-9 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.)

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.)

Martha Jones

Woman Who Walked the Earth — When Martha Jones enters, investigate. (Create a Clue token. It's an artifact with "{2}, Sacrifice this token: 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.)

Star Whale

Flying, vigilance
Other creatures you control have ward {2}.
Suspend 6—{1}{U} (Rather than cast this card from your hand, you may pay {1}{U} and exile it with six time counters on it. At the beginning of your upkeep, remove a time counter. When the last is removed, you may cast it without paying its mana cost. It has haste.)

Ryan Sinclair

Whenever Ryan attacks, exile cards from the top of your library until you exile a nonland card. You may cast the exiled card without paying its mana cost if it's a spell with mana value less than or equal to Ryan's power. Put the exiled cards not cast this way on the bottom of your library in a random order.
Doctor's companion (You can have two commanders if the other is the Doctor.)