So this isn't an easy question to answer, by which I mean to say there are some consistent threads which we can look at which relate together, but what I don't want to do is push a thesis stating this is why these countries joined together as the Axis and led to World War II, as it isn't some black and white comparison.
The thread that I'm going to trace here is colonialism, and how the late unification (in the case of Italy and Germany) and the late entry of Japan into the global network ("Unification" is not what you really mean here. The Tokugawa Shogunate rules over a unified Japan since the 17th century. Rather we're speaking of the "Opening of Japan" and the Meiji Restoration in the 19th century), placed that at a disadvantage in their attempts to establish themselves as colonial powers with the desire to play "catch-up".
Focusing on Germany first, while some of the various German states did make attempts at overseas possessions, they quite tiny and ultimately unsuccessful. The German colonial empire only began to take shape in the late 19th century, under Bismarck, following unification. Locked out of much of the world as it had already been claimed by more established powers, the German Colonial Empire included assorted Pacific islands, a small toe-hold in China, with the bulk of territory coming from Africa, the last continent available for European exploitation by the late 1800s. I won't dwell too much on the realities of German colonial rule as they aren't germane to the topic, merely to point out that it was exploitive, destructive, and genocidal, as is generally the rule here.
In any case though, the German Colonial Empire paled in comparison to those who had gotten into the 'game' earlier, and in any case, it was lost to them in the aftermath of World War I when their various colonial possessions were parceled out to the victors. This now comes to the core of the matter, namely Hitler, the rise of Nazism, and the idea of Lebensraum. There are multiple frames by which we can view the idea of 'Living Space' that formed a core component of the Nazi ideology, but for our purposes, the frame of colonialism is important. Hitler's aim was the creation of a new German Colonial Empire which, as he detailed in the Second Book, would help fuel the competition with the United Stated he envisioned down the line. Although the core focus now was on a colonial empire based in Europe, focused on the fertile lands to the east of Germany, in the long run he also had an eye for rebuilding an overseas colonial empire as well.
It is perhaps ironic that the actual value Germany's colonies had brought prior to World War I was somewhat marginal, and their actual loss perhaps even beneficial in the long term, but that ignores what they did provide, which was if nothing else a sense of pride and accomplishment, the banner of 'Colonial Power' being a important component in the self-image of the country as a First Rate Power. The driving force of German colonialism in the 1880s versus the 1930s were not exactly the same. If anything the failure of the earlier colonial empire informed Hitler that the focus on Europe was a necessity before turning eyes overseas. But they do exist on the same spectrum and the nationalist force driving German colonialist ideology spans from its foundation into the Nazi era.
Italy is not dissimilar. Unifying only in the latter half of the 19th century, Italy too was late to the colonialism party, able, in those few decades, to nibble at some of the crumbs from the shrinking Ottoman Empire, but then also quite stymied in their attempt to take Ethiopia following their 1896 defeat at Adawa. Nevertheless, Italy did have herself a small African Empire, but like Germany, one that paled in comparison to European colonial powerhouses. And although being on the winning side meant she retained it going into the interwar period, it did not reach the grandeur many wished. Enter, stage right Mussolini. The focus here is on Mussolini's desire for a New Roman Empire, a powerful Italy reborn, and as with the original one, a vast colonial empire was part of that vision, and component that was quite lacking.
Italy would again attempt, with somewhat greater success, to take Ethiopia, the lone remaining "candidate" for conquest in Africa, as well as annexing Albania in early 1939, and with the rumblings of war, hoping for her share of the spoils, would launch several misguided attempts at further conquest, attempting to push into British held Egypt as well as bully Greece into ceding territory, both of which ended in disasters requiring German military assistance.
Again though, the focus here is on the threads of colonialist thought, which was, as in Germany, a central component of the Fascist Party's politics and ideology, but by no means originated with them. And in neither case of Germany or Italy should we say that colonial dreams were caused by late unification, as at best we can really only say that the ability to attempt their fulfillment was delayed in manifesting itself until they existed as unified states. It is a tenuous thread at best, for that matter, as it is a thin connection and one which is quite hard to play effective counter-factuals with, but at the very least we can say how the German and Italian peoples and leadership conceptualized colonialism and their desire for it was shaped in part by their late entry into the game as colonial powers, and that those were some of the factors that we continue to see in the lead up to World War II.
You'll notice I've left off Japan in the previous paragraph, which was for several reasons. The first is that they did not unify late. As I noted at the beginning, I believe you are conflating the Shogunate with disunity. But there is a similar thread in Japan's level of isolation up to the mid-19th century, and a similar game of 'catch-up' with the West that does have echoes of the two previously discussed nations. However this feeds into the second issue, which is that I'm less versed in Japanese pre-war colonial ideology so am simply less comfortable expanding too much on it. Certainly I can give the basics, which sketch out as their invasion of Korea in 1894, the clash with Russia in 1905, and their continued, growing antagonizing of China throughout the period. Their decision to challenge the Western Powers directly in 1941 was part of their imperialistic vision of the 'Greater East Asia Co-Prosperity Sphere', which would remove the influence of the Western powers (principally the US, Britain, France, Netherlands) and place Japan in the drivers-seat of East Asia and Oceania, through a mix of subservient puppet-states, colonies, and annexed territories.
Again though, that is only a rough sketch, less to dwell on the details than to paint the broader picture as relates directly to the question, namely that all three countries, Japan, Italy, and Germany, had, to various degrees, a drive to, as they saw it, catch up and assert their place at the forefront of nations on the backbone of colonial imperialist acquisition of territory. The specific aims varied, but it is a consistent theme that can be seen. And of course correlation is hardly causation. By no means should any of this be to say that any of this placed them on the path they did, it is simply a consistent thread that the three happen to share.
Sources
Berghahn, Volker. 2017. German Colonialism and Imperialism from Bismarck to Hitler 1. German Studies Review 40, (1) (02): 147-162
Palumbo, Patrizia, ed. A Place in the Sun : Africa in Italian Colonial Culture from Post-Unification to the Present. Berkeley: University of California Press, 2003.
Smith, Woodruff D. "The Ideology of German Colonialism, 1840-1906." The Journal of Modern History 46, no. 4 (1974): 641-62.
Weinberg, Gerhard L.. Germany, Hitler, and World War II. Cambridge University Press, 1995.
The common reason for participation of these countries in WW2 was dissatisfaction with the world order that existed in the 1930s, along with internal factors. Fascism (and Nazism and the ideology the military radicals followed in Japan) stressed a lot how successful countries were counties that were big, in the geographical sense, or had a lot of colonies. The UK, the US and France were like that. Lebensraum, or spazio vitale, or the Great East Asia Co Prosperity Sphere, were all about controlling a larger space than what the countries had at, for example, 1920.
So why were these countries small or had a few colonies instead of being big or having lots of colonies? The fact that they were latecomers to national unification plays a part in it. Germany and Italy came late to the colonial game in part due to this late national formation, and the colonies they got were smaller than the ones France or the UK got, for example, relative to their size in Europe.
Regarding Japan it is not so much about national unification. You can argue that Oda Nobunaga, Toyotomi Hideyoshi or, especially, Tokugawa Ieyasu, had unified Japan in the late 16th or early 17th century. But the country isolated itself for 200 years and when it opened it took a lot of time to catch up technologically to the others. When the Japanese started acquiring colonies (Taiwan in 1895, for example) it was late in the colonial game, and after Taiwan and Korea, there was some animosity among the Western powers toward they getting too many concessions from China. Most Western powers agreed with the US’s Open Door Policy, which didn’t allow much outright land-grabbing. Some concessions (control over port cities) yes, but not much more than that.
After WW1, Germany lost its colonies and a chunk of its territory, territory which it had controlled (part of Poland, for example) or in which German nationals lived (again, Poland and Czechslovakia). Hitler was all about unifying the Germans in different countries and acquiring space for them to live in as he thought they deserved, as the best Europeans in the world. In his manifestoes this meant acquiring territory in Eastern Europe, especially Russia. He’d do things differently from the Second Reich (the Imperial Germany) that tried to find colonies in Africa or Asia.
You’ll notice that two of the powers you mentioned fought on the side of the Triple Entente during WW1 (Italy and Japan). Some very important sectors in these countries were not satisfied with the Versailles treaty. The Italians didn’t get all that they wanted. They got some territory from Austria-Hungary, but not Dalmatia nor part of the German colonies. Dissatisfaction with that, along with economic crisis, fueled the rise of Mussolini and the fascists.
With Japan the anger towards the Western powers occurs because the Racial Equality Clause was not approved in Versailles (due to Australian pressure). But, as with Italy or Germany, the rise of aggressive politics, like fascism, takes a while and happens as the economy of the country worsens in the mid-1920s. Nevertheless, the “betrayal” of Western powers, not treating Japan equally after it achieved status as a regional power (Triple Intervention of 1895, what they considered unfavorable intermediation of the US in the Treaty of Portsmouth of 1905, rejection of Racial Equality Clause in Versailles in 1919 and putting Japan in a lower tier than the UK and the US in the Washington Naval Treaties), was one of the reasons mentioned for Japan to abandon the international order as it existed in the League of Nations, for example.