Japan wasn't relinquishing its empire
From various sources available today we could conclude that there was no general plan for "retreat" into home islands, and defense of it. Some units were withdrawn, but overall it was expected from Japanese armies abroad to fight where they were, and local defensive plans to that end were drawn. Let's go example by example :
Kwantung Army was perhaps largest intact Japanese formation. Although best units from it were transferred elsewhere during the war, it was still relatively large - in the summer of 1945 (before Soviet attack) it had around 700 000 troops. It is presently unknown did Japanese knew about agreements from Tehran and Yalta conferences (USSR to attack Japan 3 months after end of war in Europe), but in spring of 1945 they did make defensive plans in case of Soviet attack. Although these plans largely incorrectly estimated Soviet intentions and main directions of the offensive, nevertheless they existed. Generally, they called for thinly held Soviet and Mongolian border, and retreat towards south and Korean border. Kwantung Army was to defend and deny Soviet entry into Korea, and wait from assistance from Japanese army in China. Although Kwantung army was relatively close to home, and could have withdrawn to Korea and possibly even across Sea of Japan to Japan proper, this option was not considered.
China Expeditionary Army was another major Japanese formation. Late in the war its strength was usually described as around 1 million soldiers, although this was sometimes disputed (strength given as 500-600 000). In any case, not only this army was not withdrawing, as late as spring/summer of 1945 it was actually engaged in offensive actions against Chinese. Examples of this include battles in North Hubei and West Hunan. Overall operational plan was to push both Chinese forces and US air power (in airfields in China) as far as possible from home islands. As we saw before, theoretically this army would help in case of Soviet attack in Manchuria, although this did not materialize historically.
Final larger formation that should be mentioned would be Southern Expeditionary Army Group. Although covering large and diverse area, and heavily engaged with Allied forces, there was no worthwhile effort to move its troops somewhere northward (pull them back at least to China, if not Japan). There were some localized efforts to abandon parts of Burma very late in war (Battle of the Sittang Bend), but overall plan was to defend as much territory as possible. Examples of this would be 28th and 33rd Army, newly created units with specific missions to fight and defend parts of Burma, which they did to best of their abilities.
What was general Japanese strategy ? Although they sensed possibility of Allied invasion of home islands, Japanese could not and would not withdraw troops from overseas possessions to mainland. Reasons range from logistical to strategical. Japan could barely feed its own population as it is. Millions of troops, that usually lived off the land at the expense of local populace, would now had to be fed by Japanese themselves. Also, occupied territories did still offer lot of raw resources useful for Japanese war industry. True, it was getting difficult to transport these to Japan proper due to Allied naval blockade (subs), but something was trickling in. It is questionable how would this blockade effect attempts of troop withdrawal, if attempted. It should be noted that lots of troops (in places like China and Burma) were also engaged with the enemy so this would also endanger possible long withdrawal. Finally, occupied territories offered some kind of bargaining chips in case of negotiations, and Japanese hoped that such negotiations would eventually take place if they held out a little more.