What initially started as a mere change of the ruler from a Polish-Lithuanian king to a Russian czar eventually led to a major russification drive.
Administratively Lithuania was divided into the area directly acquired by Russia in 1795 and the area acquired from Prussia after the Napoleonic wars (in 1815). The latter was part of the nominally autonomous Kingdom of Poland and lived under the Napoleonic Code whereas the earlier was directly ruled by the Russian Empire.
In 1831 and 1863 the local nobility led revolts against the Russian rule attempting to restore the Polish-Lithuanian Commonwealth. Both were crushed despite some initial successes and their leaders were dispossessed. Some of the Lithuanian countryside and cities were then settled by Russians.
In the year 1832, the Vilnius University was closed. By the year 1865, printed Lithuanian language was banned. A policy of “Restoration of the Russian beginnings” was initiated as the Russian propaganda claimed that before Polonization the Lithuanian lands were, in fact, Russian.
The Roman Catholic Church was persecuted, with some church buildings torn down and some others handed over to the Russian Orthodox church. New Russian Orthodox churches sprung in the New Towns of the largest cities. The Uniates, regarded as schismatic Orthodoxes, were disbanded altogether. Mikhail Muravyov, nicknamed “The hangman”, was made the governor-general of ethnically Lithuanian governorates.
The persecutions failed to defeat Lithuanians. Knygnešiai (literally “bookcarriers”) smuggled the banned Lithuanian books from the Lithuania Minor (a historical fact declared to be completely unique by UNESCO). Illegal Lithuanian-language schools were set up in villages. Catholic priest Motiejus Valančius led the Abstinence Movement aimed at resisting the Russian policy of weakening the masses through making them addicted to alcohol.
It was during the late 19th century when the popular idea of liberation among ethnic Lithuanians switched from restoration of the Grand Duchy of Lithuania to an establishment of a smaller independent state on the Lithuanian ethnic lands, leaving the rest of the former Grand Duchy to the Belarusian, Ukrainian, and Polish ethnic states. These events (altogether known as the Lithuanian National Revival) tamed the long-term assimilation-induced decline of the Lithuanian-inhabited area and their share therein.
Economically Russia was backward compared to the Western Europe and while there was some infrastructure development, such as the Saint Petersburg-Warsaw railroad of 1861 that went through Vilnius, this was far from the Western standards. Moreover, the official class division of the society was rigorously supported by the state and only in the year 1861 the farmers ceased to be regarded as a property of the local nobles.
Unlike Latvia (where Riga was among the 5 largest cities of the Russian Empire) Lithuania was expected by the Russians to remain an agricultural hinterland. The industrialization and urbanization that defined 19th century elsewhere in Europe, therefore, remained limited but the towns and cities were still growing much faster than ever before.
Lithuanians seeking industrial jobs migrated elsewhere: some to the major cities of the Russian Empire such as Riga or Saint Petersburg, others to the USA. In 1900 there were more Lithuanian speakers in Riga and Chicago than in any city in Lithuania (where the few cities that existed were dominated by Polish speakers and Jews).
In Lithuania Minor, the cities were largely German while some Lithuanian towns and villages gradually Germanized over the century. In spite of this Lithuania Minor, technologically advanced and devoid of discriminatory Russian policies, remained a fortress of Lithuanian National Revival.
The Russian Empire started to crumble in 1904 when it lost the war to Japan and had to give in to some demands of its minorities. Lithuanian language was permitted once again and the Lithuanian countryside sprung up with new Roman Catholic church spires.
In 1915 the Germans captured Lithuania-proper during the First World War. In 1917 Russia surrendered to Germany (after the war hardships led to a revolution in Russia) and renounced any claims to the eastern coast of the Baltic Sea, while the subsequent German losses in the Western Front led to a possibility to declare independence of Lithuania on February 16th, 1918.