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.)

Rory Williams

Partner with Amy Pond
First strike, lifelink
The Last Centurion — When you cast this spell from anywhere other than exile, exile it with three time counters on it. It gains suspend. Then investigate. (Create a Clue token. It's an artifact with "{2}, Sacrifice this artifact: Draw a card.")

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.)

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 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.

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.

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