Where Germany and Japan allies? Or did they just happen to go to war at the same time?

The ideological basis of the alliance was opposition to Communism. Germany and Japan were the founders of the Anti-Comintern Pact in 1936, which opposed the Communist International. Italy joined in 1937.

The European and Asian wars began as separate wars. The Japanese war in China actually began in 1937. Italy and Germany created a military alliance in 1939 with the Pact of Steel. At the time, Japan did not join, as it did not have an interest in a European war. Germany had annexed Czechoslovakia and Italy had annexed Albania, while Britain and France were now guaranteeing the security of Poland and Greece. In 1938-1939, Japan was engaged in a border conflict with the Soviet Union in Mongolia/Manchuria and did not want to fight the Western powers. Germany reached a neutrality pact with the Soviet Union in 1939, before the two countries occupied Poland, starting the European war. But after the fall of France in 1940, the three Axis powers formed the Tripartite Pact, recognizing each others' sphere of influence and supporting each others' efforts to overthrow the existing world order:

Japan recognizes and respects the leadership of Germany and Italy in the establishment of a new order in Europe.

Germany and Italy recognize and respect the leadership of Japan in the establishment of a new order in Greater East Asia.

They further undertake to assist one another with all political, economic and military means if one of the Contracting Powers is attacked by a Power at present not involved in the European War or in the Japanese-Chinese conflict.

Japan, Germany and Italy affirm that the above agreement affects in no way the political status existing at present between each of the three Contracting Powers and Soviet Russia.

The obvious conclusion to be drawn from these key points of the text is that the Tripartite Pact was aimed at the emerging Anglo-American alliance, and at the United States specifically. In the summer of 1941, Germany invaded the Soviet Union, but Japan and the Soviet Union signed a neutrality pact. Yet, when the United States declared war on Japan, Germany and Italy declared war on the United States (although arguably they were not obliged to, since Japan was not attacked by the US). It was not until the final month of the war, August 1945, that the Soviet Union declared war on Japan. In general, the European and Asian-Pacific theaters of World War II were separate and Japan did not coordinate much with the European members of the Axis.