The failure to build fortifications in Vallisaari backfired in 1808, when Sweden and Russia were at war, and the Russians besieged Viapori. The Russians brought dozens of artillery pieces to Vallisaari – Vallisaari overlooked Viapori, after all, and provided an excellent field of fire. Viapori surrendered to the Russians. Sweden ceded Finland to Russia, and Finland became an Autonomous part of the Russian empire.

Vallisaari was renamed Aleksanterinsaari ("Alexander Island"), in honour of the tsar. The Russian period became the heyday of fortification construction. Viapori was an important element in the defences of St. Petersburg, the capital of imperial Russia. The Russians also began developing fortifications in Vallisaari. However, it was not until the Crimean War, which broke out in 1853 between Russian and an alliance formed by the Ottoman Empire, Britain, France, and Sardinia, that the construction gained real impetus. In Vallisaari and Kuninkaansaari, batteries, or gun emplacements, were built.

In 1854, a Franco-British naval force entered the Baltic Sea. The military build-up in Helsinki and Viapori was intensified. In August 1854, the allies sailed into Helsinki waters, bombarding Viapori. The sea off Vallisaari was covered by smoke and fire, and Viapori sustained extensive damages.

Soon after the war, an imposing battery named the Alexander Battery was built in Vallisaari, to demonstrate Russia's military might. Changes in Russia's foreign policy and developments in military technology were soon reflected in the Alexander Battery. Originally, the battery's guns had been placed in casemates, or impact-proof, covered emplacements. However, by the early 1870s, they were moved to the top of the embankment. The casemates were built into shelters for troops and storehouses, and the brick walls were covered with thick sand embankments.

In 1906, the islands off Helsinki became a scene of events that foreshadowed the Russian revolution. The mutineers took over Vallisaari and Kuninkaansaari. The mutineers shelled Viapori from Kuninkaansaari, with success. However, despite their original winning position, the explosion of the gun powder supply in Kuninkaansaari and shelling by the Russian navy tipped the scales against the mutineers, causing panic among them and their ultimate defeat. Dozens of lives were lost in this conflict, some of them in executions following the fighting.

For the pilots in Vallisaari, a new Luotsitalo pilot house was completed by 1878, and the pilots were ordered to relocate to the building. In 1910, Hylkysaari island was designated as a new base for the pilots, but, due to a lack of premises, some of them still remained in Vallisaari. The last pilots left the island as late as in the early 1920s.

In the years preceding WWI, the batteries in Vallisaari were modernised with concrete constructions, and a gunpowder magazine was built in the middle of the island. During the world war, a brick barracks for officers was built, in addition to a number of storage buildings. However, Vallisaari and Kuninkaansaari began to lose their importance in Russian maritime defence. The focus of the defences was moved out to sea. The Russians began to build fortifications in the outer archipelago of Helsinki, including the islands of Isosaari, Kuivasaari, Harmaja, and Rysäkari.

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