There is a theme in Halo, of old conflicts being fought anew at a time far in the future. The most obvious instance of this lies in the Forerunner-Flood War, in which the activation of Halo halted the war for 100,000 years until the descendants of the Forerunners met what Flood had survived in hibernation. In addition, it also would appear that most human conflicts in the Halo universe are based on historical wars, primarily those related to America.
The Interplanetary War, a series of conflicts in the twenty-second century, has its roots in both World War II and the Cold War. The war pitted the United Nations against two enemy factions known as the Koslovics and the Frieden, organizations composed of Russian communists and German fascists respectively. They are likely each based on the Soviet Union and Nazi Germany, with whom America fell into conflict, as did the United Nations, on which it was also likely to have been based, with its similar enemies. With the defeat of the Koslovics and the Frieden came the formation of the United Earth Government, dominant over all of the human population, from what was once the United Nations.
In the latter half of the twenty-fifth century, however, some of the Outer Colonies came to think that their local governments could do a better job of taking care of their populations than could the UEG. After their requests to secede were denied, numerous groups in support of secession went to war with the UNSC in a conflict known as the Insurrection, which has similarity with the American Civil War.
The primary conflict is that of the Human-Covenant War, which has many similarities to various historical conflicts. The most obvious, I believe, is to the currently ongoing conflict America has with certain Middle Eastern countries such as Afghanistan and Iraq. In some respects, the Covenant resembles radical Islam, which America opposes in real life just as the UNSC opposes the Covenant in Halo.
However, other parallels can be made with the Crusades, in which Christian aggressors waged a religious war primarily against Muslims over occupation of Jerusalem. Jerusalem is considered to be of extreme religious significance to both cultures, the city heavily referred to in the Bible and the Koran. Similarity can be drawn to the Covenant invasion of Earth, in which the Covenant take the place of the Christians and the humans as the Muslims.
The Covenant similarity to the Abrahamic religions of humanity is obvious, providing an interesting parallel. The aggressors fight on the basis of a religion very similar to the people they attack, over the occupancy of a land (planet) considered holy due to the presence of ancient holy sites. This may, however, simply be a coincidence, as Bungie appears reluctant to portray the humans as anything other than American.
Another war that could have served as inspiration for the Human-Covenant War is the previously mentioned WWII. Unlike the other connections, which are primarily made up of my own speculation, there is some canonical basis to this one. In Halo: The Fall of Reach, McRobb expresses a worry that Reach will turn out like Pearl Harbor.
Pearl Harbor, for those unaware, was an American naval base on Honolulu, Hawaii that was attacked by Japan in 1941, bringing America actively into WWII. In this, the Covenant is compared with Imperial Japan, a culture with which it does share some notable similarities. For instance, much of the Sangheili warrior culture appears modeled on the romantic notion of the samurai as it appears in popular culture. In addition, both the Sangheili and Jiralhanae armor bears striking resemblance to that of the samurai. The Prophet of Truth, ultimate leader of the Covenant and aspiring god, could be compared with Japanese Emperor Hirohito Showa, who claimed to be a god in human form.
The Human-Covenant War is compared with WWII again in ilovebees, when Colonel Herzog speculates that ONI knew planets Troy and Harmony were to be attacked by the Covenant and let the attacks occur in order to keep the Covenant unaware their transmissions were being monitored, bringing up a similar incident in WWII in which the British forces cracked Germany’s code and had to make their own sacrifices. In this comparison, the Covenant are not Japan but rather their Axis ally Nazi Germany. It is easy to see the link between power-hungry, genocidal Prophet of Truth and Adolph Hitler, and perhaps this is where such inspiration originated.
This is all primarily speculation, so don’t take this as strict fact. I, however, view it all as likely to have influenced Bungie as they concocted their wonderful world. And in the end, Bungie’s own spin changes the scenario radically enough so that anything that could apply to these historical wars does not in the unique environment they designed. Their own story ultimately becomes the important one.