As with other Anno games, the player starts as leader of an unarmed country which must colonize and expand in the game world. While the player expands their in-game territory, other computer controlled rivals are also expanding and strengthening their countries. As the player progresses through the game, they have access to lodge activities and troops which allow them to invade and ultimately to defeat other players. Anno 1404 features an updated interface, bigger islands and worlds to explore, a sandbox mode, and other features new to the Anno series

The player is sent to administer a fief granted to him by the Emperor, in the Occident. The Emperor is unwell and Lord Richard Northburgh, cousin and treasurer of the Emperor, is building a magnificent Cathedral to pray for the Emperor's health. Meanwhile, Lord Richard Northburgh teaches him the basics of Anno 1404, and requests assistance in procuring goods for the Cathedral's construction, until Guy Forcas is sent by Cardinal Lucius to prepare for a crusade. Lord Northburgh is suspicious of the great secrecy over the mission. Marie d'Artois is given command of the crusader army and Brother Hilarius, a local abbot, is ordered by Forcas to bless their weapons. The player is then ordered to build a harbor for the ships, near a settlement suspiciously named "Orphanage". Brother Hilarius comments on this until Northburgh realizes that Forcas kidnapped children from Inglebeck, Marie d'Artois' settlement. The settlement is abandoned when the vanguard of the crusaders and Marie d'Artois leaves.

A storm then starts and the ships bearing the children sail away, with the player and Northburgh in pursuit. The player then attempts to befriend the Grand Vizier of the Sultan after coming across the Orient and rescue the children. Northburgh finds out that Cardinal Lucius attempts to overthrow the Emperor, but is then arrested by Forcas and the Crusader army arrives. Marie d'Artois raids several Oriental settlements, and with the aid of the Grand Vizier, Al Zahir, Karim, a Caravan master and the scholars of the Academy of Wisdom, the player finds a wreck of a corsair ship. The scholars translate a logbook found in the wreck and the player finds a key, and with the help of an Oriental fleet, a strongbox. Inside the strongbox is a treaty between Cardinal Lucius and the corsair leader, written in blood, which provided the Crusader fleet safe passage through the corsair infested waters should the Cardinal Human trafficking children. The player, having been given a flag of truce from Brother Hilarius, who was in a local monastery, and delivers the message to Marie d'Artois. Marie and the vanguard of the Crusader fleet attempts to leave the Crusader harbour, but is under heavy fire from Forcas' fleet and the main Crusader army. Marie's flagship attempts to hold Forcas off but is heavily damaged and Marie is wounded. With the aid of his own fleet, Marie's fleet and Oriental battleships, the Player sinks the Crusader fleet and Forcas goes down with his flagship.

However, the much more numerous rearguard of the Crusader fleet, lead by Lucius himself, arrives. The player then flees to Marie's fortress-city, Edenisle, and attempts to stop Lucius' invasion of the city harbour. A ship is sent to Al Zahir to request for aid, and Barnabas, Marie's former battle-instructor and his robber barons join the player after Marie, wounded, gives command of the city to the player. After constant pounding by Lucius' heavy warships, and constant sorties by Lucius' troops, Al Zahir's fleet arrives, and the city is evacuated. The city is razed by Lucius. Al Zahir leads the refugees into the heartland of the Orient, where rumours say that the Occidental Emperor is spending his last days there, due to his mysterious illness. The player tries to request an audience, but Abbess Hildegard refuses entrance to anyone unless they are the Emperor's relative. The player, after asking a few locals, discover that Richard Northburgh is imprisoned in an Assassins' fortress. Meanwhile, Marie d'Artois has returned to the heartlands of the Occident and Phillipe Lamour, a trusted man in her service, constantly returns to the Orient with news of the battle between Marie and Lucius and requests supplies and reinforcements. The player, with the aid of Al Zahir's miners, break Northburgh out of the prison, and aid Hekata the witch and her two sisters to create a potion named "the Essence of Life". The Emperor drinks the potion, which the player and Northburgh gave him during their audience, and then Northburgh and the player leave for the Occident.

Once the player and Northburgh return to the Occident, they find the player's settlement razed, as is most of Northburgh and Marie's cities. A mad Lucius starts the construction of a Imperial Cathedral, like the one Northburgh started building, to show the Church's power on Earth and to become the most powerful man in the Church. The player tries to rebuild Northburgh's city and secure the supplies for the construction of the Cathedral. Unfortunately, Lucius had either destroyed or shut down all of the construction industries. Marie tries to assemble a fleet to destroy Lucius, and the player's Oriental allies give the player specialists to quicken the construction of the player's Cathedral. Lucius' spies attempt to sabotage the Cathedral many times, but fail. However, Lucius had seized the Academy of Wisdom and its scholars, and so the player "acquired" Lucius' Colours from Karim in exchange for some paper, and delivers a strongbox from Al Zahir to the unsuspecting Lucius, who forwards it to the Academy. The chief researcher opens the strongbox and a sandstorm destroys Lucius' buildings and troops on the island. The grateful scholars give the player a tome which speeds up the construction of the Cathedral significantly, and when it is finished, the player's city has a mysterious plague, like the illness that befell the Emperor. Karim, the caravan master, exchanges the last sample of the "Essence of Life" which he had acquired from the witches, and Northburgh distributes it among the city's residents, healing them. Then the Emperor and the Imperial fleet arrives, and the player is ordered to destroy Lucius' fleet with a combined fleet consisting of the player's, Marie's and the Imperial fleet and destroys Lucius' fleet utterly. Lucius is captured, who attempts to convince the player to spare him, is brought before the Emperor, who has Lucius condemned and sent to prison, but it is not shown in the game how Lucius met his fate. The Emperor, Northburgh, Marie, Al Zahir and the Sultan thank the player and the player is given the title "Saviour of the Realm".

MINIMUM:

· OS: Windows® 2000/XP (SP2)/Vista

· CPU: 3 GHz Intel Pentium®4 or similar

· RAM: 1 GB RAM

· GPU: DirectX® 9.0c compatible mit 128 MB with Shader 2.0

· Minimum disc space: 6 GB

· DVD-ROM: Only needed for installation

· Soundcard: DirectX® 9.0c compatible

· DirectX®: Version 9.0c

· Input Devices: Mouse, Keyboard

RECOMMENDED:

· OS: Windows XP (SP 3), Windows XP (64-bit), Windows Vista (SP1), Windows Vista (64-bit)

· CPU: Intel Core2 Duo E4600 (2,4 GHz) or AMD Athlon64x2 4800+ (2,5Ghz)

· RAM: 2 GB RAM

· GPU: DirectX® 9.0c compatible mit 512 MB with Shader 3.0

· Minimum disc space: 6 GB

· DVD-ROM: Only needed for installation

· Soundkarte: DirectX® 9.0c compatible

· DirectX®: Version 9.0c

· Input Devices: Mouse, Keyboard