Trans 9/WMG

The Daligig are secretly evil.
Look at the facts. Stacy was originally programmed as a prison ship. Even despite the severity of the situation, she still refuses to tell cast members the most basic of things, and bitchslapped Cortana into forgetting something very important that is probably going to come back and bite everyone in the ass. And who knows what "Punishment" is supposed to be? Cool and Unusual Punishment? Disproportionate Retribution? Fate Worse Than Death? Room 101?


 * We know what Punishment is now. That knowledge really does NOT go to ANY length to deny the guess.

Stacy is a Time Lord.
Someone prove me wrong.

It Was Only a Dream
Everything the crew has experienced is just a simulation created in Stacy's systems. Computer personalities created from the memories of the podded refugees are running through millions of possible scenarios at once, to determine which crew members can work together to defeat the Ohm. Simulations where one person is awake; or one million: fighting every possible enemy and each other. Once all the simulations are run and the ideal crew has been chosen for 'real' awakening, the computer personalities will be erased as no longer necessary.

The Ohm: Saviors of the Multiverse!
Thread Walkers (people who can change their own destiny, such as the crew of the Trans-9) are a deadly threat to the Multiverse. Their slightest action can create an entirely new universe, which is dramatically weakening all of space/time across all realities. The Ohm have discovered this, and must save the Multiverse by eliminating some of the universes, or the entire thing will collapse. If the crew of the Trans-9 manage to wipe out the Ohm and restore their home dimensions, they will in fact destroy all realities, everywhere, forever.

The Ohm are attacking to protect themselves
Basically, the Ohm are pre-emptively striking at any universe that may eventually become a threat to their existence. Why? Maybe someone attacked the actual Ohm and killed members of the race first. Possibly one of the previous crews.

Stacy is an Ohm construct or possibly an Ohm herself
The Daligig captured an Ohm ship-type, stripped out its brain, and used its (possibly bioformed?) body for their own purposes. The Ohm found out and are trying to get revenge on whoever killed one of their own. Obviously they would think this might be the crew of Stacy, yes?

(Re)Boot to the Head
Whenever a fictional universe is rebooted, its original form needs to be cleared from the hearts and minds of the Metaverse. The Ohm are manifestations of the power of that change, let loose to literally devour the old universe and make way for the new. Obviously, their paychecks are signed by DC.

Annihilus is the leader of the Ohm and the ultimate antagonist of the whole game.
The Ohm seek to destroy all reality and, by extension, all life. Somehow, Annihilus broke through the Fourth Wall, somehow conquered Chaos and the entirety of the Black Lantern Corps, and amplified the strength, capabilities, and bloodlust of his Annihilation Wave.

Nemo is The Dragon to whoever controls the Ohm.
He shows up right after  to steal the guy's blood for a very nefarious purpose, managed to easily take on Supergirl and Superboy at the same time, and is the leader of the Catastrophists, whose goal is to ensure that all life is wiped out. Guy like that does not just show up out of nowhere at the right time.