The following article contains spoilers from DCeased: War of the Undead Gods #1, on sale now.
Supergirl's absence in the pages of DC's zombie saga has finally been explained. Unfortunately, DCeased: War of the Undead Gods #1 (by Tom Taylor, Trevor Hairsine, Andy Lanning, Rain Beredo, and Said Temofonte) reveals that Kara was sent to New Genesis, a planet recently infected by the Anti-Life virus. As a result, she got infected, providing the forces of the dead with an invaluable weapon against the surviving heroes.
While the new Justice League may have restored their lost loved ones and have two Supermen on their side, Kara's unique place in her family makes her a singular threat. She has been noted to absorb solar radiation faster than her cousin, potentially making her more powerful. In addition, the Anti-Life virus has a mind of its own and is capable of planning ahead -- and it will likely take advantage of this situation.
Proof of this can be found in how it controlled Superman once he had been infected. Rather than pursue the survivors as they fled Earth, the virus had him take shelter inside the sun. This was a tactical retreat, given that Superman had been injured in the initial fight and lost an arm. However, given that he returned five years after being infected, it suggests that the Anti-Life virus was preparing for an even bigger battle and merely trying to muster as much strength as it could.
Indeed, leaving Superman in the sun all those years exponentially increased his power, but it raises the question of why it didn't use him to stop the Justice League when they returned to Earth. Unless, Superman was never intended to be used in a battle for one planet, but all existence. Now, Supergirl seems to be in a similar predicament. It took Superman five years in the sun to rival the combined might of the Justice League's strongest members. But since Kara can absorb solar energy faster, then she might be able to reach that same potential in a significantly shorter amount of time.
This presents a problem for the Justice League. They're already up against an army of undead gods, but a fully powered Kryptonian alone could rival or trounce them. Now, they have one who is capable of gaining even more power faster than any other Kryptonian. To make matters worse, her possible inability to control herself makes her a terrifying wildcard. The Justice League really have their work cut out for them.
Their only shred of hope is that if it comes down to a fight between the Kryptonians, it is two against one. However, Kara's opponents will be holding back, in an effort to save their family member. But, it won't be Kara they're fighting, it will be the Anti-Life virus, which is unlikely to show them the same mercy. At the moment, the potential outcome of the fight is up in the air, but it seems to be shifting more and more in favor of their enemies.