The Third Doctor

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

Tangletrove Kelp

Ward {2}
At the beginning of each combat, other Clues you control become 6/6 Plant creatures in addition to their other types until end of turn.
{2}, Sacrifice Tangletrove Kelp: Draw a card.

Nuka-Cola Vending Machine

{1}, {T}: Create a Food token. (It's an artifact with "{2}, {T}, Sacrifice this artifact: You gain 3 life.")
Whenever you sacrifice a Food, create a tapped Treasure token. (It's an artifact with "{T}, Sacrifice this artifact: Add one mana of any color.")

Tireless Tracker

Landfall — Whenever a land you control enters, investigate. (Create a Clue token. It's an artifact with "{2}, Sacrifice this artifact: Draw a card.")
Whenever you sacrifice a Clue, put a +1/+1 counter on Tireless Tracker.

Alquist Proft, Master Sleuth

Vigilance
When Alquist Proft, Master Sleuth enters, investigate. (Create a Clue token. It's an artifact with "{2}, Sacrifice this artifact: Draw a card.")
{X}{W}{U}{U}, {T}, Sacrifice a Clue: You draw X cards and gain X life.

Jaheira, Friend of the Forest

Tokens you control have "{T}: Add {G}."
Choose a Background (You can have a Background as a second commander.)

Five Hundred Year Diary

Five Hundred Year Diary enters tapped.
{T}: Add {U} for each Clue you control.
{2}, Sacrifice Five Hundred Year Diary: Draw a card.

Morska, Undersea Sleuth

You have no maximum hand size.
At the beginning of your upkeep, investigate. (Create a Clue token. It's an artifact with "{2}, Sacrifice this artifact: Draw a card.")
Whenever you draw your second card each turn, put two +1/+1 counters on Morska, Undersea Sleuth.

Lonis, Cryptozoologist

Whenever another nontoken creature you control enters, investigate.
{T}, Sacrifice X Clues: Target opponent reveals the top X cards of their library. You may put a nonland permanent card with mana value X or less from among them onto the battlefield under your control. That player puts the rest on the bottom of their library in a random order.

In Too Deep

Split second (As long as this spell is on the stack, players can't cast spells or activate abilities that aren't mana abilities.)
Enchant creature, planeswalker, or Clue
Enchanted permanent is a colorless Clue artifact with "{2}, Sacrifice this artifact: Draw a card" and loses all other abilities. (It's no longer a creature or planeswalker.)

Academy Manufactor

If you would create a Clue, Food, or Treasure token, instead create one of each.

Madame Vastra

Partner with Jenny Flint (When this creature enters, target player may put Jenny Flint into their hand from their library, then shuffle.)
Madame Vastra must be blocked if able.
Whenever a creature dealt damage by Madame Vastra this turn dies, create a Clue token and a Food token.

Piper Wright, Publick Reporter

Whenever Piper Wright deals combat damage to a player, investigate that many times. (To investigate, create a Clue token. It's an artifact with "{2}, Sacrifice this artifact: Draw a card.")
Whenever you sacrifice a Clue, put a +1/+1 counter on target creature you control.

Confront the Unknown

Investigate, then target creature gets +1/+1 until end of turn for each Clue you control. (Create a Clue token. It's an artifact with "{2}, Sacrifice this artifact: Draw a card.")

Lonis, Genetics Expert

Evolve (Whenever a creature you control enters, if that creature has greater power or toughness than this creature, put a +1/+1 counter on this creature.)
Whenever one or more +1/+1 counters are put on Lonis, investigate that many times.
Whenever you sacrifice a Clue, put a +1/+1 counter on another target creature you control.

Merchant of Truth

Flying
Whenever a nontoken creature you control dies, investigate.
Clues you control have exalted. (Whenever a creature you control attacks alone, that creature gets +1/+1 until end of turn for each instance of exalted among permanents you control.)

Graf Mole

Whenever you sacrifice a Clue, you gain 3 life.

Ongoing Investigation

Whenever one or more creatures you control deal combat damage to a player, investigate. (Create a Clue token. It's an artifact with "{2}, Sacrifice this artifact: Draw a card.")
{1}{G}, Exile a creature card from your graveyard: Investigate. You gain 2 life.

Adrix and Nev, Twincasters

Ward {2} (Whenever this creature becomes the target of a spell or ability an opponent controls, counter it unless that player pays {2}.)
If one or more tokens would be created under your control, twice that many of those tokens are created instead.

Lazav, Wearer of Faces

Whenever Lazav, Wearer of Faces attacks, exile target card from a graveyard, then investigate. (Create a Clue token. It's an artifact with "{2}, Sacrifice this artifact: Draw a card.")
Whenever you sacrifice a Clue, you may have Lazav become a copy of a creature card exiled with it until end of turn.

Armed with Proof

When Armed with Proof enters, investigate twice. (To investigate, create a Clue token. It's an artifact with "{2}, Sacrifice this artifact: Draw a card.")
Clues you control are Equipment in addition to their other types and have "Equipped creature gets +2/+0" and equip {2}.

Case of the Pilfered Proof

Whenever a Detective you control enters or is turned face up, put a +1/+1 counter on it.
To solve — You control three or more Detectives. (If unsolved, solve at the beginning of your end step.)
Solved — If one or more tokens would be created under your control, those tokens plus a Clue token are created instead. (It's an artifact with "{2}, Sacrifice this artifact: Draw a card.")

Astrid Peth

Whenever Astrid Peth enters or attacks, create a Food token.
Brand-new Sky — Whenever you sacrifice a Clue or Food, Astrid Peth explores. (Reveal the top card of your library. Put that card into your hand if it's a land. Otherwise, put a +1/+1 counter on this creature, then put the card back or put it into your graveyard.)

Jenny Flint

Partner with Madame Vastra
First strike
Training (Whenever this creature attacks with another creature with greater power, put a +1/+1 counter on this creature.)
Whenever you sacrifice a Clue or Food, put a +1/+1 counter on another target creature you control.