1801 Battle of Copenhagen:

In January Nelson was promoted to Vice-Admiral of the Blue flag and became second Commander in Chief of the Channel Fleet. Emma and Sir Hamilton now lived with all luxuries at Nelson's house at his cost. In all parts of the house, there were paintings of Emma and Horatio. Sir William's state of health became more and more hopeless. At the end of this month two children were born to Emma, but one died shortly after its birth. The other one survived and was named Horatia. Because of a possible scandal, Nelson and Emma invented the story that Horatia was the daughter of a dead sailor. Nelson and Emma adopted Horatia as their daughter. Nelson was very glad about the birth, but its secrecy made him sad, because later his relatives wouldn't accept Horatia as a legal heiress.

Preparing for Copenhagen:
Nelson received an order to become second commander in chief under Sir Hyde Parker, who had order to sail in the Baltic Sea to destroy the alliance of the Baltic states: Russia, Denmark and Sweden. He sailed to Yarmouth in St. George, where Parker's fleet was assembling.

After his arrival, Nelson noticed that Sir Hyde was inexperienced in battle with ships of the line, but he had been in the service of the Royal Navy longer and so Nelson had to accept his command angrily. He tried to force Sir Hyde to a faster departure of the fleet.
On the 26th of March, the British fleet had arrived in the waters of Copenhagen, but the Danes gave the signals that they would leave the Baltic Alliance and started to arrange the defence of their capital. In front of the capital, the Danes had moored seven ships of the line and 11 hulks with guns. They had the Fort of Tekron in the middle of their moored line. Sir Hyde ordered Nelson to attack the Danish line according to Nelson's own plan.
This situation of the Danish line looked very similar to Abukir, but in the bay of Copenhagen, the waters were much more dangerous than in Abukir because of many shallows. In addition, Nelson couldn't attack the Danes from all sides, because the waters behind the Danish line weren't deep enough for ships of the line. The Danes were also better sailors than the French. In this battle, the Danes had to defend their capital, and that's why they used all their power and every man to make Nelson attack harder. Casualties on the Danish side were easily replaced by fresh men from land.

The Flagship "Elephant":
Nelson got 11 ships of the line, including his new flagship "Elephant", 6 frigates , some brigs and some bomb-vessels. Sir Hyde kept some ships as reserve and moored north of the Danish capital. One day before the battle, Nelson ordered to control and measure waters in front of the Danish line.

On 2nd of April, Nelson attacked the Danes, but already during the deployment of his ships he lost 2 ships of the line, because they sailed on ground. The guns shot on both sides and Nelson's ships suffered a lot of hits. At 13:00 Sir Hyde, who was watching the battle, signalled the signal Nr.39 "Disturb the battle". He did this, because he was afraid of too strongly damaged ships. In further battles he might also fight against the Russian and Swedish ships, and with damaged ships he would have no chance to win.

Nelson saw this signal, but put the telescope in front of his blind eye and said to his officers he couldn't see anything. His crew understood the trick and signalled to Sir Hyde "Understood."

Nelson used this trick because of his intuition, which said the Danes would surrender.
But the British forces couldn't continue the fighting for further time, so Nelson sent a message under the white flag to the Danish prince:

"Lord Nelson had directions to spare Denmark when no longer resisting; but if the firing is continued on the part of Denmark Lord Nelson will be obliged to set on fire all the floating batteries he has taken without having power of saving the brave Danes who have defended them.
Dated on board His Britannic Majesty's Ship Elephant, Copenhagen Roads
April 2nd , 1801
Nelson and Bronte, Vice admiral under the commandof Sir Hyde Parker "

This message was a kind of blackmail for the Danish prince. He had the alternative of either rescuing the capital or seeing his men die. He ordered an armistice and sent representatives on board of the Elephant. The British fleet withdrew and prepared its vessels to shoot on the capital.

On the 9th of April, both sides signed a 14-week long armistice. While the armistice was being signed, the Danes already knew that the founder of the Baltic Alliance, Tsar Paul, had been killed and his son Alexander would cooperate with England.

On the 5th of May, the fleet got dispatches that Nelson had been created Viscount and should replace Sir Hyde as Commander in Chief in the Baltic Sea. Soon Nelson sailed to Reval to fight against the Russians, but the Russians didn't want to fight and arranged meetings with English ambassadors. They signed a paper on the abolishment of the Baltic Alliance. Nelson's mission was successful, and he sailed back to England in bad health.