After the skirmish in Grosvenor House, the Rogans and G are making their way through the ruined London, unaware that a particularly agile and quick zombie is pursuing them with a machete. Just as it tries to attack G, he is saved by fellow AMS agent Gary Stewart with a shotgun. Upon the group's arrival at AMS Headquarters, where an evacuation seems to be in progress, they are instructed by Kate Green to not leave their things with the Quartermaster and keep going straight to the Tower of London. G and the Rogans arrive to meet up with King "Hal" and Director Lindbergh, where they learn what's causing all the excitement: a mass of zombies and mutants making their way out of the Isle of Dogs Fear Foundry. The mines at the Ethelred Line, London's final line of defence, are holding the monsters back, but the group are easily outnumbered. Lindbergh suspects that the Resurrection Men are behind it, but G denies it, putting it down to those who got the survivors into such a desperate situation, the sinister East of Eden... unaware that as he speaks, he is being watched by a mysterious crippled man, who thinks aloud that 'it was all over long ago'...
After Thomas and Sophie Rogan share a dance (much to the embarrassment of Lisa Rogan and the disdain of an American agent), the agents head to the Underground and engage the zombies. Some time afterward, Lisa uses explosives to destroy a Tube station with the threats inside. The heroes find themselves outside One Canada Square but are distracted when mud monsters arise from the river and begin attacking those assembled. With the island now "one big target factory", G runs off and advises Gary to "aim for the head".
The gang soon find themselves inside, faced with a giant tree. Whilst distracted an agent is impaled and killed by a C-controlled monster. The antagonist ensures his enemies that this is all part of an attempt to revert the world into a greener haven, but the Rogans don't buy it. A fierce battle erupts with Lisa using a bomb to destroy the tree.
In the aftermath, the villains are forced to back off and let the AMS agents return to London - their leader is worried by Rogan's coded implication that AMS have identified the group's agents and are planning a counterstrike. Back in the City, where Hal is commanding the defensive actions, the Ethelred Line is in danger of being overrun - only for the Resurrection Men to arrive in helicopter gunships to 'save the day'. But as Rogan regroups his men at Wapping, Agnes Reid makes her demands clear to the exhausted City: "we're hear to discuss the terms of your surrender."
- The crippled man in One Canada Tower is taken from the third and fourth video games. East of Eden are an original concept (unnamed until Parts 3/4).
- Hal is intended to be an adult Prince Harry.
- The Ethelred Line is named after King Ethelred/Aethelred the Unready, who couldn't stop the Danes tearing through most of England but did keep hold of London.
- Charnel House has so far drawn negative criticism from fans, who found the story difficult to get into or even understand, so much so that even those who are fans of the House of the Dead games are confused. An alarming amount of readers have outright stated they have refused to read later chapters, making this one of the least popular Sega Superstars strips in history.
- Gary's usage of the word 'ass' has also been criticised.
- The story has been particularly hard to get into for those who live outside of London, including some locations that aren't even named in the comic.
- The cliffhanger in part 2 has been criticised as unclear (G is meant to be charging One Canada Tower, hence "aim for the head").
The previous House of the Dead story was Resurrection Men. This is the most recent story.