Crack in Time

Vanishing 3 (This enchantment 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 Crack in Time enters and at the beginning of your first main phase, exile target creature an opponent controls until Crack in Time leaves the battlefield.

Rotating Fireplace

Rotating Fireplace enters tapped with a time counter on it.
{T}: Add an amount of {C} equal to the number of time counters on Rotating Fireplace.
{4}, {T}: Time travel. 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.)

Wilfred Mott

Look to the Stars — At the beginning of your upkeep, put a time counter on Wilfred Mott. Then look at the top X cards of your library, where X is the number of time counters on Wilfred Mott. You may put a nonland permanent card with mana value 3 or less from among them onto the battlefield. Put the rest on the bottom of your library in a random order.

Four Knocks

Vanishing 4 (This enchantment enters with four time counters on it. At the beginning of your upkeep, remove a time counter from it. When the last is removed, sacrifice it.)
At the beginning of your first main phase, draw a card.

Scholar of New Horizons

Scholar of New Horizons enters with a +1/+1 counter on it.
{T}, Remove a counter from a permanent you control: Search your library for a Plains card and reveal it. If an opponent controls more lands than you, you may put that card onto the battlefield tapped. If you don't put the card onto the battlefield, put it into your hand. Then shuffle.

Grateful Apparition

Flying
Whenever Grateful Apparition deals combat damage to a player or planeswalker, proliferate. (Choose any number of permanents and/or players, then give each another counter of each kind already there.)

Out of Time

When Out of Time enters, untap all creatures, then those creatures phase out until Out of Time leaves the battlefield. Put a time counter on Out of Time for each creature that phased out this way.
Vanishing (At the beginning of your upkeep, remove a time counter from this enchantment. When the last is removed, sacrifice it.)

Thrummingbird

Flying
Whenever Thrummingbird deals combat damage to a player, proliferate. (Choose any number of permanents and/or players, then give each another counter of each kind already there.)

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 Regenerations Restored, scry 1 and you gain 1 life. Then if Regenerations Restored has no time counters on it, exile it. When you do, take an extra turn after this one.

Trenzalore Clocktower

{T}: Add {U}. Put a time counter on Trenzalore Clocktower.
{1}{U}, {T}, Remove twelve time counters from Trenzalore Clocktower and exile it: Shuffle your graveyard and hand into your library, then draw seven cards. Activate only if you control a Time Lord.

Wibbly-wobbly, Timey-wimey

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.)
Draw a card.

Infinite Hourglass

At the beginning of your upkeep, put a time counter on Infinite Hourglass.
All creatures get +1/+0 for each time counter on Infinite Hourglass.
{3}: Remove a time counter from Infinite Hourglass. Any player may activate this ability but only during any upkeep step.

The Moment

At the beginning of your upkeep, put a time counter on The Moment.
{2}, {T}: Untap target creature you control. It phases out until The Moment leaves the battlefield.
{3}, {T}: Destroy each nonland permanent with mana value less than or equal to the number of time counters on The Moment. Then sacrifice The Moment. Activate only as a sorcery.

The Millennium Calendar

Whenever you untap one or more permanents during your untap step, put that many time counters on The Millennium Calendar.
{2}, {T}: Double the number of time counters on The Millennium Calendar.
When there are 1,000 or more time counters on The Millennium Calendar, sacrifice it and each opponent loses 1,000 life.

The Girl in the Fireplace

(As this Saga enters and after your draw step, add a lore counter. Sacrifice after III.)
I — Create a 1/1 white Human Noble creature token with vanishing 3 and "Prevent all damage that would be dealt to this creature."
II — Create a 2/2 white Horse creature token with "Doctors you control have horsemanship." (They can't be blocked except by creatures with horsemanship.)
III — Whenever a creature you control deals combat damage to a player this turn, time travel.

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.)

As Foretold

At the beginning of your upkeep, put a time counter on As Foretold.
Once each turn, you may pay {0} rather than pay the mana cost for a spell you cast with mana value X or less, where X is the number of time counters on As Foretold.

Flesh Duplicate

You may have Flesh Duplicate enter as a copy of any creature on the battlefield, except it has vanishing 3 if that creature doesn't have vanishing. (A permanent with vanishing 3 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.)

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.

Time Beetle

Skulk (This creature can't be blocked by creatures with greater power.)
Parallel Universe — Whenever Time Beetle 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.)

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.)

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.

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 Chronozoa dies, if it had no time counters on it, create two tokens that are copies of it.

Danny Pink

Mentor (Whenever this creature attacks, put a +1/+1 counter on target attacking creature with lesser power.)
Creatures you control have "Whenever one or more counters are put on this creature for the first time each turn, draw a card."