
Captain America: Civil War introduced a famous Marvel Comics super maximum security prison to the MCU in The Raft, which was created to incarcerate enhanced individuals underwater. After Captain America: Brave New World, The Raft houses five MCU supervillains, including Baron Zemo, The Leader, Thaddeus Ross, and two characters from Netflix's Defenders Saga. The Raft was the site of Captain America 4's cryptic post-credit scene that saw Tim Blake Nelson's Samuel Sterns tease Avengers: Doomsday with a warning of "others," hinting at Robert Downey Jr.'s Doctor Doom and Multiversal threats to come.
During Marvel Zombies Episode 2, the superhero survivor gang arrives at the City on the Sea, which was ultimately revealed to be the MCU's Raft. Formerly a prison for the most formidable offenders, the Raft was repurposed as a sanctuary for survivors in the apocalypse, shielded(ish) from the zombies by the water.

Randall Park's Jimmy Woo described the City on the Sea as "one of the last safe places on Earth," as the undead, as far as they knew, couldn't swim. Having picked up Marvel Zombies' survivors from the New Orleans checkpoint, which is presumably one of many, the former prison set sail to safety.

At the New Orleans security checkpoint, the arriving group was asked if they brought a "tribute," for which they provided a herd of cows. As such, it appears that would-be City on the Sea residents must provide something to the community that must be approved by its ruler - an unexpected MCU villain.
Surprisingly, the boss running the City on the Sea turned out to be Baron Zemo, with Rama Vallury replacing Daniel Bruhl as the MCU villain. Acting as his second-in-command was Wyatt Russell's John Walker, who never became U.S. Agent.

As the Marvel Zombies universe didn't branch from the Sacred Timeline until 2018, the events of Captain America: Civil War presumably still took place. This means Zemo was likely among the prisoners at the Raft before the outbreak began, and he assumed control to convert it into the City on the Sea.
The City on the Sea converted the Raft from a prison into something of a sanctuary, whose inhabitants are allowed as much food as they wish and sleep on comfortable bunk beds in the former cells. The city's inhabitants are clearly also fond of their leader, as they all chanted "Zemo" before he delivered a speech.

As it turns out, the City on the Sea was keeping a "dirty little secret," as Zemo was even aware of the one threat to his sanctuary - Zombie Namor and the undead Talokanil who could swim their way to the sailing city.
The Civil War villain declared to the newcomer survivors, "He's hungry, and we've learned the only way to stop him is to feed him," ejecting their cell to feed them to the underwater kingdom, only for them to make their way back.

Ultimately, Namor and the Talokanil made their way on board and slaughtered the residents of the City on the Sea and flooded its halls. As such, Florence Pugh's Yelena Belova became one of 24 casualties in Marvel Zombies, going down with the ship so the other survivors could escape.
The Raft Might Be Key to the Avengers' Survival in Secret Wars
Circling back to Earth-616, Baron Zemo, Thaddeus Ross/Red Hulk, and Samuel Sterns/The Leader are the most important prisoners still aboard the Raft.
Currently, none of those characters has been reported or reliably rumored to be coming back to the MCU anytime soon, leaving it uncertain when the Raft could be revisited again after its Multiversal role in Marvel Zombies.
Interestingly, the Raft has been featured in the last three Captain America-related projects - Civil War, The Falcon and the Winter Soldier, and Brave New World. As such, the prison could be revisited again if Captain America 5 happens, which may be unlikely after Brave New World possibly lost money for Disney.
Some have speculated that the Raft could gain a new purpose in the MCU with Avengers: Doomsday. As 2015's Secret Wars featured a Life Raft that could survive the final Incursions and the end of the Multiverse, it's possible the prison could get some upgrades to fill this purpose in the MCU adaptation.
After all, fans have just seen the Raft repurposed as a sanctuary for survivors of a zombie apocalypse, why not do the same for the end of the Multiverse?