Bah! Doom has no need to consider Loki as commander!

Doom is chosen to lead the villains in Secret Wars #1
Doom alone will whip “uncooperative” jerks into line at the kitchen table.

Doom provides the tools to command a cohort of conniving villains set to evade the enemy, pillage on attacks, and endure in the long game. Each combat, Doom will filter our cards and grant evasion. As we discard lands, our opponents’ life will drain under Doom’s brilliant wrath.
Bah!
Doom Calls on Molecule Man

Doom confronts Molecule Man in Secret Wars #1
Of all the new cards released in Doom Prevails, Molecule Man is the most exciting. Totally broken alongside a Sensei’s Divining Top and other library stacking and draw effects, Molecule Man allows you to cast the first card drawn each turn for free.

Many who upgrade Doom Prevails end up cutting Molecule Man due a lack of support in the deck. Molecule Man is great, their arguments contend, but not here.
This is true. Out of the box, we only get Currency Converter, Lethal Scheme, three cycling lands, and a Baron Strucker, HYDRA Overlord plus Progenitor’s Icon combo to trigger Molecule Man on our opponents’ turns. Of those options, none can trigger three times per turn cycle.

Molecule Man trying to be good in Secret Wars #1
We can do better. We can help Molecule Man be a good villain.

Compulsion, Trade Routes, and Tectonic Reformation provide inexpensive recursive draw to trigger Molecule Man on each of our opponents’ turns while enabling our other discard synergies, including Doom.
Late in the game, Trade Routes can double as our win condition as we pick up our lands from play and discard them to drain each of our opponents.
Living Laser, Red Ghost, Intangible Genius, Typhoid Mary, Fractured (as well as our mayhem and unearth villains) also benefit from these inclusions.

Ivora, Reckoner Bankbuster, and Azor’s Gateway—while limited to just once per turn cycle—grant a little extra power for Molecule Man while being strong cards in their own right.
An additional six ways to support Molecule Man out of ninety-nine cards.
Doom needs more power.
Make It So
Q: What do all of our Molecule Man enablers have in common?
A: They cost 2!

Muddle the Mixture transmutes for any of our Molecule Man enablers while doubling as cheap interaction. In a pinch, we can alternatively pick up Terminate or Batroc the Leaper to control problematic creatures or planeswalkers. In a dream scenario, Batroc alongside Sanctum of the Sun for a modest thirty mana could deal fourteen damage to each of fourteen targets.

Batroc kicks everybody in Captain America #252
In addition to a tutor for enablers. We will add one tutor for Molecule Man himself.

Ethereal Usher transmutes for Molecule Man (or Lady Loki’s Manifestation if we want cards now) while providing late game unblockability to trigger our villain attack bonuses.
While we are tutoring, we will add a few more twos and sixes for Doom.
Doom’s Plan
Bah!
Doom has had enough of Molecule Man! It is time for Doom’s plan!
Out of the box, we get one plan—Glorious Purpose—and it features Loki. Bah!
If the deck includes a plan, it must be Doom’s!

Doom covets a Cosmic Cube in Sub-Mariner #49
Doom Reigns Supreme and Construct a Cosmic Cube are auto-includes for flavor, mechanics, and budget.

With villain typal synergies, connive synergies, and a promise of cosmic domination, Doom is pleased. To ensure Doom’s plan proceeds unthwarted, we recruit draft chaff The Masters of Evil to fetch what we need.

Muddle the Mixture and Ethereal Usher deliver their transmutational work once again. It is a hard way to do it, but the promise of the Cosmic Cube’s power is irresistible to Doom!
Friendly Help

Leader introduces Doom to M.O.D.O.K. in Fall of the Hulks
As long as we are villains, let’s recruit the best of the worst.

Leader, Super-Genius and M.O.D.O.K. both provide excellent value and board presence for Doom. Together, they are near unstoppable. (We pay three life to connive with M.O.D.O.K., triggering Leader. We draw two cards and discard one. We pay three life, draw two cards, then discard one. We…) When we are ready, M.O.D.O.K. will even return some of the life to us on attacks, with additional returns from our Iron Monger, Sadistic Tycoon.
Cuts

Doom takes by force in Marvel Super Heroes #20
Doom has no need for that which he has no need!
Cut everything that does not enable Doom’s plan or that belongs in draft cards left behind at the LGS for the bulk bin. Bah!
Helmut Zemo, Mastermind
Extract Power
Killmonger, Ruthless Usurper
Endless Ranks of HYDRA
Lady Loki, Agent of Chaos
Syphon Mind
Moonstone, Harsh Mistress
Chaos Warp
Kang, Temporal Tyrant
The Frightful Four
Prowler, Clawed Thief
Madame Hydra
Damocles Base, Sword of Kang
Other Considerations

Villains assemble in Secret Wars #1
There are endless options for ways to enable Doom’s plan. Cryptcaller Chariot (as a zombie team in a can), Marchesa, the Black Rose (helping our villains always return), and Norman Osborn (everything Doom wants, really), were all close inclusions.

Cryptcaller’s Chariot and Marchesa just didn’t seem flavorful enough for this upgrade. And, their lack of villain typal synergies meant they couldn’t make the team.
Norman Osborn would have made the cut if he didn’t want $20 to join the team.
Villains… sheesh.
Cleanup Step
We have taken Doom Prevails, added support for Molecule Man, focused in on Doom’s plan, and recruited a few more villains to up our power.
As always… Bah! Doom has no need for Table for Four’s fun, kitchen table Magic.

Doom is expelled from school in Fantastic Four Annual #2