In August 1798 the Battle of the Nile took place. Nelson wiped out the French fleet while it was at anchor in the shallows. 38,000 French soldiers were stranded. The French defeat allowed the formation of a second coalition, by restoring European confidence in Britain. Europe decided to attack France while she was weakened.

A three-pronged attack was planned on France, by Britain, Austria and Russia:

• Britain would attack through Holland
• Austria would attack through Italy
• Russian would attack France through Switzerland

The French campaign in Egypt and Syria (1798–1801) was Napoleon Bonaparte's campaign in the Ottoman territories of Egypt and Syria, proclaimed to defend French trade interests, to establish scientific enterprise in the region and ultimately to join the forces of Indian ruler Tipu Sultan and drive away the British from the Indian subcontinent. It was the primary purpose of the Mediterranean campaign of 1798, a series of naval engagements that included the capture of Malta. The campaign ended in defeat for Napoleon, and the withdrawal of French troops from the region.

In 1798, Paul I gave General Korsakov command of an expeditionary force of 30,000 men sent to Germany to join Austria in the fight against the French Republic. At the beginning of 1799, the force was diverted to drive the French out of Switzerland. In September 1798, with the consent of the Turkish government, a Russian fleet entered the Mediterranean, where the emperor Paul, appointing himself protector of the Order of St. John of Jerusalem, intended to liberate Malta from the French. Admiral Fyodor Ushakov was sent to the Mediterranean in command of a joint Russian-Turkish squadron to support General Alexander Suvorov's upcoming Italian and Swiss expedition (1799–1800). One of Ushakov's main tasks was to take the strategically important Ionian Islands from the French. In October 1798 the French garrisons were driven from Cythera, Zakynthos, Cephalonia, and Lefkada. It remained to take the largest and best-fortified island of the archipelago, Corfu. Russia signed an alliance with Turkey on January 3, 1799. Corfu capitulated on March 3, 1799.

The Battle of Stockach occurred on 25 March 1799, when French and Austrian armies fought for control of the geographically strategic Hegau region in present-day Baden-Württemberg. In the broader military context, this battle constitutes a keystone in the first campaign in southwestern Germany during the Wars of the Second Coalition,

In the Battle of Magnano on 5 April 1799, an Austrian army commanded by Pál Kray was a clear-cut victory by Kray over the French, with the Austrians sustaining 6,000 casualties while inflicting losses of 8,000 men and 18 guns on their foes. The defeat was a crushing blow to French morale and prompted Schérer to plead with the French Directory to be relieved of command.

The Battle of Winterthur (27 May 1799) was an important action between elements of the Army of the Danube and elements of the Habsburg army, commanded by Friedrich Freiherr von Hotze, during the War of the Second Coalition, part of the French Revolutionary Wars. The small town of Winterthur lies 18 kilometers (11 mi) northeast of Zürich, in Switzerland. Because of its position at the junction of seven roads, the army that held the town controlled access to most of Switzerland and points crossing the Rhine into southern Germany. Although the forces involved were small, the ability of the Austrians to sustain their 11-hour assault on the French line resulted in the consolidation of three Austrian forces on the plateau north of Zürich, leading to the French defeat a few days later.

In March, Masséna's army occupied Switzerland, preparing an attack against Tyrol through Vorarlberg. However, the defeats of French armies in Germany and Italy forced him to return to the defensive. Taking over Jourdan's army, he pulled it back into Switzerland to Zürich. Archduke Charles pursued him and drove him back west at the First Battle of Zurich. The French general André Masséna was forced to yield the city to the Austrians under Archduke Charles and retreat beyond the Limmat, where he managed to fortify his positions, resulting in a stalemate. During the summer, Russian troops under general Korsakov replaced the Austrian troops.

When Charles left Switzerland for the Netherlands, the allies were left with a smaller army under Korsakov, who was ordered to unite with Suvorov's army from Italy. Masséna attacked Korsakov, crushing him at the Second Battle of Zurich. Suvorov with a force of 18,000 Russian regulars and 5,000 Cossacks, exhausted and short of provisions, led a strategic withdrawal from the Alps while fighting off the French. Allied failures, as well as British insistence on searching shipping in the Baltic Sea led to Russia withdrawing from the Second Coalition. Emperor Paul recalled the Russian armies from Europe.

An Anglo-Russian force of 32,000 men landed in North Holland on August 27, 1799, captured the Dutch fleet at Den Helder on August 30 and the city of Alkmaar on October 3. Following a series of battles at Bergen on September 19 and Alkmaar on October 2 (also known as 2nd Bergen), they faced the French and Dutch armies at Castricum on October 6. Following a defeat at Castricum, the Duke of York, the British supreme commander, decided upon a strategic retreat to the original bridgehead in the extreme north of the peninsula. Subsequently, an agreement was negotiated with the supreme commander of the Franco-Batavian forces, General Guillaume Marie Anne Brune, that allowed the Anglo-Russian forces to evacuate this bridgehead unmolested. However, the expedition partly succeeded in its first objective, capturing a significant proportion of the Batavian fleet.

During the siege of Genoa the Austrians besieged and captured Genoa. However, the smaller French force at Genoa under André Masséna had diverted enough Austrian troops to enable Napoleon to win the Battle of Marengo and defeat the Austrians.

The Treaty of Amiens temporarily ended hostilities between France and the United Kingdom at the end of the War of the Second Coalition. It marked the end of the French Revolutionary Wars.

Key Findings:

• Under the treaty, Britain recognized the French Republic. Together with the Treaty of Lunéville (1801), the Treaty of Amiens marked the end of the Second Coalition, which had waged war against Revolutionary France since 1798.
• Britain gave up most of its recent conquests; France was to evacuate Naples and Egypt. Britain retained Ceylon (Sri Lanka) and Trinidad.
• The territories left of the Rhine are part of France. - Daughter republics in the Netherlands, Northern Italy, and Switzerland
• The Holy Roman Empire is obliged to compensate the German princes for the lost territories left of the Rhine. - The treaty is generally considered to be the most appropriate point to mark the transition between the French Revolutionary Wars and the Napoleonic Wars, although Napoleon was not crowned emperor until 1804.
• The consequences of the Second Coalition had proved fatal to the Directory. Blamed for the resumption of hostilities in Europe, it was compromised by its defeats in the field and by the measures required to repair them. Conditions were now ripe for the military dictatorship of Napoleon Bonaparte, who landed at Fréjus on October 9. A month later he seized power by the coup of 18–19 Brumaire Year VIII (November 9–10, 1799) to make himself first consul.