Gustav Vasa I helped Sweden break free from the Kalmar Union and win its indepedence against Denmark and Norway. He became King of newly indpendent Sweden (which included Finland), established a new dynasty and led to a reformation of the church making Sweden Lutheran. He vastly strengthened the state and built a modern army which was the envy of the region. Sweden began its own expansion and conquered Estonia. In 1587 the heir to the Swedish throne Sigismund Vasa (shown in this painting) became the new ruler of the Polish Lithuanian Commonwealth in part due to his catholic Polish mother. After his father King John III died, Sigisumund promised to unite Sweden with Poland and Lithuania promising to respect Lutherans as the new King of Sweden - but in 1597 Swedish aristocrats led by Sigismund's uncle Duke Charles IX rebelled.

In 1598, Sigismund landed in Sweden with an army of Polish, German and Hungarian mercenaries but was defeated at the battle of Linköping and forced to retreat by superior Swedish forces. Charles IX (shown here insulting the corpse of Sigismund supporter Klaus Fleming), prepared for a counter invasion of the Polish Lithuanian Commonwealth with 15000 men conquering Estonia and moved quickly southwards into Livonia. In 1601 the famous Polish military commander Chodkiewicz was called back from Moldavia to defend against the Swedish invasion. He fought a decisive victory in Kokenhausen in 1601 killing 3000 Swedes largely due to the famous Winged Hussars cavalary, also known as the Angels of Death. General Zamoyski arrived with an additional 12000 men which forced Charles IX back into Estonia and ultimately a full retreat. A few years later Sweden came back with 4 larger armies with a goal to capture Riga.

Chodkiewicz moved his armies near Kirchholm on hills facing off against the numerically superior Swedes. Through clever planning, tactics and a feint retreat, Chodkiewicz led Charles IX into a trap which decimated the Swedish armies by Winged Hussars and Tatars. This total victory forced Charles IX to flee to his landing camp near Riga. In total the Commonwealth forces only lost 100 men with 200 injured while over 8000 Swedes were killed or captured. They abandoned the siege of Riga and fled back across the Baltic Sea to Sweden. Ironically Chodkiewicz's unpaid troops and mercenaries mutinied shortly afterwards and abandoned him preventing him from capitalizing on the total victory - the war ultimately ended in a stalemate for both sides.

During this conflict, both famine and plague hit Riga. The soldiers had consumed all the food and the people of Riga and nearby areas suffered. To make matters worse a plague epidemic hit and made the city a ghost town. Mass grave pits were established including several near St. Gertrude Church, located outside the city walls of the old Riga town. There was also a burial pit and traditional individual graves in this church graveyard from this time. Some bodies were found to have died of natural causes or sieges of the city. However several were analyzed and tested positive for Yersinia Pestis - plague - which had devastated the city in 1601.