Ghost Earth II: Atomic City is the second book of the series.
After an ambush that destroyed the Great Lakes Citadel, James Anderson travels from the Camden Ruins he accidentally teleported himself to into Metropolitan City. The entire city undergoes a massive assault in the time between the collapse of the citadel & James' arrival in the ruins & is currently fighting a massive battle between the Alliance for the Survival of Humanity & the League of Imperial Cybernetic Hybrids. At the very same time, a small division of the Alliance is leading a major attack on the Dark Nest that proves futile as everyone involved is killed.
The same characters from the last story: James Anderson, Victor Underwood, Eddie Smith, Commander Jackson, Emily Love & Maureen & Luke. Maureen is not directly seen, but communicates with James through a communicator. In the middle of the story, Cyber Erol makes his first appearance to the Alliance by interrupting a conversation between James & Maureen. He later appears in his fully recreated self & during his first appearance, he revealed himself as the leader behind the Imperials. During the course of the book, Draco is introduced as the second-in-command to Cyber Erol & is responsible for the operations the Imperials run trying to take over Metropolitan. Grievous, the third-in-command of Cyber Erol, is not seen until the climax of the story when the Imperial War Factory is directly over the city & the Imperial Guard is attacking the square. Commander Jackson dies shortly before this by decapitation. Core, the shadowghost leader, meanwhile, is mentioned, but not seen.
After teleporting himself to the Camden Ruins by accident, James Anderson receives a call from Eddie Smith to escort a Cargo Train to Metropolitan for the Alliance. Upon arrival, James is nearly arrested & imprisoned by the Imperials. He escapes & roams the city.
Meanwhile, the Alliance has split itself in two. The largest half has stationed itself in Metropolitan City while the smaller half went to New York II. During this time, the New York II Alliance quickly mobilizes to the Dark Nest in the area of the mountains west of the Wastelands. Core, the shadowghost leader, called upon the Imperials to destroy the invasion with them. During the trip to the Nest, the Imperial War Factory passed directly over Metropolitan & dispensed tons of troops of Imperials. The Imperial squadrons took most of the city, but were stopped by the Alliance from taking Logan Square, which is home to their new base, the Academic Military Research Institute. The Imperials, led by Cyber Erol, a recreated cyborg version of the late Erol, are dispatched via air trains to the city & they're overseen by Draco, Cyber Erol's second-in-command.
James manages to stumble his way through Imperial lines & meets up with his girlfriend, Emily Love & Eddie Smith at the border between the Alliance-controlled Logan Square & Imperial-controlled Metropolitan, which are separated by a barrier that prevents humans from passing through, only Imperials & shadowghosts can pass back & forth. Smith tells James to go south into the city & find the home of the Underground Alliance, a civilian's version of the Alliance meant for evacuating the city of civilians & attempting an overthrow of Draco's hold on the city. James arrives at the headquarters to find that it's his cousin's home. Luke, who has been running the Underground, tells James about the events of the city & how most of the civilians have been evacuated, among them being Maureen. James then goes out to destroy three Imperial Blast Bots that were sent by Draco to destroy the house. James destroys them & then when he returns to the house, Luke gives him another assignment. Out in an alleyway behind the house, the Imperials are excavating an entrance to the legendary Metropolitan Catacombs. Luke tells James to investigate & in effect, James explores the Catacombs, eventually riding a subrail to another entrance at the base of the Mine Bridge, a major bridge meant to connect to another city in New Jersey. Maureen calls James & tells him to destroy the operations of the Imperials on the bridge. In the end, James ends up destroying the Mine Bridge itself. Before it collapses, he uses a warp gate back to the house. On the orders of Commander Jackson, James descends into the basement of the house to enter the Catacombs again to reach the Academic Military Research Institute. James rides another subrail & when he emerges from the Catacombs, he finds the entrance is in the Metropolitan Cathedral. To protect the holy place from being attacked by the shadowghosts or Imperials in an ambush, James blows up the entrance with dynamite.
Draco, meanwhile, is concerned as to the reports about James' deeds on the Imperials. During a call with Cyber Erol, Draco requests that an Imperial zeppelin be sent in to hover over the Institute as an off-ground base of operations that is inaccessible to any of the Alliance should they succeed in penetrating the barrier separating the Institute from the rest of the city. Erol, angry that Draco has failed, threatens to demote his second-in-command & even come to the battle personally to see that the Alliance falls if Draco cannot end the battle soon.
James meets up with his friends in the Institute. However, he is forced to protect Logan Square from an attack involving all Imperial forces present. The attack is stopped by James & the Alliance. During a call with Maureen afterwards, Cyber Erol interrupts the transmission & reveals himself to James & the others present in the room. At the same time, Draco launches another attack to catch the Alliance off guard when the Imperial dirigible appears over the city. As Draco is being escorted to the zeppelin, the Imperials attack both the Skylab & Time Tower, two vital sections of the Institute. It is revealed to the Alliance that the bottom of Time Tower holds another entrance to the Catacombs, which is actually linked to the Imperial Fortress. James destroys the Imperials in Time Tower & then rescues Vincent from the Imperials in the Skylab. James later escorts monks to the Cathedral as the Square is suddenly attacked. While James defeats the Imperials, shadowghosts end up kidnapping the monks & bringing them to Draco. Meanwhile, Cyber Erol arrives in the battle on the zeppelin as he relocates Draco back to the Imperial Fortress due to his failure.
The Alliance manages to breach the security of all the barriers surrounding Logan Square, allowing them to regain control of area surrounding the square, but are faced with major casualtys. Because the Catacomb entrance in Time Tower had been destroyed, James is forced to enter the Imperial Fortress through the front door. He fights his way to the main security room, where he tethers the zeppelin to the Fortress. James climbs the tether & explores the zeppelin. He meets Cyber Erol in the middle of it & faces his former ally for the first time. During the battle, part of the zeppelin is destroyed & collapses while Erol escapes to another area of it. He eventually escapes to the Fortress, though this is not known to the Alliance. James returns to the Skylab when he learns that the dirigible wasn't destroyed & the Skylab was under attack again. James activates the Sky Destroyer & blows up the zeppelin. Angry at the loss of the zeppelin, Commander Jackson is kidnapped by the Imperials. The monks who were kidnapped revealed to Draco how the shadowghosts can take control of the church to prevent exorcism by spilling the blood of a human on the altar, which if the blood is from a murder or execution, the church would be desecrated & the powers of it's scriptures would be surrendered to the shadowghosts. Jackson is later taken to the Metropolitan Cathedral, where he is beheaded by the shadowghosts. The Alliance soon learns of this & Eddie Smith is declared the new general.
At around the same time that James was destroying the zeppelin, the shadowghosts & Imperials finished off the invasion by scouring the area outside the Dark Nest & killing the last of the Alliance soldiers. The Nest is protected by a barrier impenetrable to anything excepting shadowghosts. With the victory secured at the Nest, the Imperial War Factory is relocated to Metropolitan, where the full might of the Imperials is thrown upon the Alliance. In one last stand to protect the city from being taken over, James & Victor fight Grievous, the leader of the Imperial Guard & the one who led the Imperials in the Dark Nest after Cyber Erol left for the city. Despite managing to win the duel, the Alliance fails to stop the Institute from being taken over. The Alliance again relocates to their old bases in New York II.
After the city is taken over, the Underground Alliance restores itself & fights for the city. Erol, aware that the city would never fall to him at this point, sends an air train out that drops an atom bomb on Metropolitan, destroying the city & everywhere within miles of it.