Estonia began moving away from Russian influence, rejecting Russia's economic model in favour of an open market and joining the European Union and NATO in 2004.

Starting the Livonian War (1558–1582), a military conflict between the Tsardom of Russia and a coalition of Denmark, Grand Duchy of Lithuania, Kingdom of Poland (later the Polish–Lithuanian Commonwealth), and Sweden.

On 24 September 1939, warships of the Red Navy appeared off Estonian ports, Soviet bombers began a threatening patrol over Tallinn and the nearby countryside.

Moscow demanded that Estonia allow the USSR to establish military bases and station 25,000 troops on Estonian soil for the duration of the European war.

The Soviet–Estonian Mutual Assistance Treaty was made for ten years: On 12 June 1940 the order for total military blockade of Estonia was given to the Soviet Baltic Fleet.

[16] The 1940 occupation and annexation of Estonia into the Soviet Union was considered illegal and never officially recognized by Great Britain, the United States, Canada, France and other capitalist democracies of the West.

Of the 32,100 Estonian men who were forcibly relocated to Russia under the pretext of mobilisation into the Red Army after the German invasion of the Soviet Union in 1941, nearly 40 percent died within the next year in the "labour battalions" through hunger, cold and overworking.

Immediately after regaining the independence, Estonia started to insist that the Soviet Union (and later Russia) should withdraw their troops from Estonian territory and that the process should be completed by the end of the year.

In response, Estonia denied the accusations of violations of human rights and invited more than a dozen international fact-finding groups to visit the country for verification.

[33] As the propaganda war and negotiations dragged on, Estonia, Latvia and Lithuania gained international support for their position on troop withdrawal at a July 1992 summit of the CSCE in Helsinki.

The final communiqué called on Russia to act "without delay... for the early, orderly and complete withdrawal" of foreign troops from the Baltic states.

The Estonian and Russian sides continued to disagree, primarily over the pace of Russia's withdrawal from the town of Paldiski, on the northern coast some thirty-five kilometers west of Tallinn.

"[43] Altogether, by the beginning of October 1939, the Soviets had amassed along the Estonia-Latvia border 437,325 troops, 3,635 artillery pieces, 3,052 tanks, 421 armored vehicles and 21,919 cars[44] According to the American author Thomas Ambrosio, the core of the current controversies lay in the Kremlin's rhetorical response to external criticisms of Russia's own democratic and human rights record, where Moscow's harsh denunciations of Estonia which are far disproportionate to Tallinn's actual policies, are intended to put the West on the defensive rather than describe the realities within Estonia[45] Russia has made three general claims based upon exaggeration or outright misrepresentation as a part of their "accuse" strategy: the human rights of the Russian-speakers were being violated; Estonia has a "democratic deficit" because it did not allow non-citizens to vote in national elections; and that rejecting the legitimacy of the Soviet occupation was equivalent to glorifying Nazism.

[citation needed] In February 2002, Russian Deputy Foreign Minister Yevgeni Gussarov presented to Estonian ambassador Karin Jaani a non-paper list of seven demands to be fulfilled by Estonia in order to improve the relations of the two countries.

It honoured Estonian soldiers who fought the Red Army during World War II and was reported as "SS monument" by some news agencies, including BBC.

The monument depicts an Estonian soldier in a German-type military uniform, and according to a journalist of the Baltic Times, with a Waffen-SS (combat SS) unit emblem.

[66] However a semiotic analysis by professor Peeter Torop of University of Tartu, consulting for the Lihula police department, concluded that no Nazi or SS symbolics whatsoever appear in the bas-relief.

[69][70] According to The New York Times: "Many Russians have accused countries once under the Kremlin’s sway, including Estonia, of not pursuing a full account of some of their citizens' collaborations with the Nazis.

According to K. Brown this vow of 'support' only aggravates attempts being made by the Russian speakers to solve their political problems independently and jeopardizes the development of healthy foreign relations between Estonia and Russia.

Estonian media have repeatedly claimed that Russian politicians called for military action against Estonia to protect the "compatriots", most recently in 2007, this accusation had been fielded against Dmitry Rogozin[75] during the Bronze Soldier crisis.

[78] The forum Development and Transition, which is sponsored by the United Nations, published an article in its newsletter in November 2005 where professor James Hughes argues that Latvia and Estonia employ a "sophisticated and extensive policy regime of discrimination" against their respective Russophone parts of the population.

[79] However, in that same newsletter Hughes arguments were opposed by former Latvian minister for social integration Nils Muižnieks who argued his views were simplistic and "similar to what Russian propaganda has been touting in international fora over the last 10 years".

The Federation Council, on 27 April, approved a statement concerning the monument, which urges the Russian authorities to take the "toughest possible measures" against Estonia.

[90] Belittling the World War II heroes' feats and desecrating monuments erected in their memory leads to discord and mistrust between countries and peoples, Russian President Vladimir Putin said on Victory Day 2007.

[91] In the days following the relocation, the Embassy of Estonia in Moscow was besieged by protesters, including pro-Kremlin youth organisations Nashi and the Young Guard of United Russia.

Estonia's president Toomas Hendrik Ilves expressed his astonishment that Russia has — despite the promises of foreign minister Lavrov — not taken actions to protect the diplomatic personnel.

On 2 May, a small group of protesters attempted to disrupt a press conference the Estonian ambassador to Russia, Marina Kaljurand was holding at the offices of the Moscow newspaper, Argumenty i Fakty, but were held back by security guards.

Additionally, Estonian government officials have called upon NATO, who has pledged their support for Estonia in the effect of Russian encroachment, by sending individuals to take place in the military exercises along the border.

[105] In September 2022, Poland, Lithuania, Latvia, and Estonia decided to close entry for Russian citizens with Schengen visas, including those issued by third countries.

During the meeting, Ilves stated that rhetoric from both countries should be toned down, with Medvedev responding by saying that the Estonian President often made harsh statements against Russia, whereas he did not do the same about Estonia.