He was wounded in 1969 by an Egyptian shell in the Suez Canal area and was discharged from active service four months later, but continued to serve in the military reserve until 1990.

In 1988, when he was called up for reserve duty in Nablus, he refused to serve on ideological grounds, as he viewed Israeli withdrawal from the occupied territories as a necessity and did not want to take part in suppressing the First Intifada, later recalling that "my sympathies were with the rebels.

[2][13] While working at The Jerusalem Post in the 1980s, Morris began reading through the Israel State Archives, at first looking at the history of the Palmach, then turning his attention to the origins of the 1948 Palestinian expulsion and flight.

Mainstream Israeli historiography at the time explained the 1948 Palestinian exodus from their towns and villages as having been driven by fear, or by instructions from Arab leaders.

[2] Another event that Morris revealed for the first time based on his archive study was the contacts between the Israeli officials and the Lebanese Kataeb Party figures, including Elias Rababi, in the period 1948–1951.

He left The Jerusalem Post in 1991 as part of a mass walkout of journalists due to a perceived right-wing turn in the newspaper and began searching for an academic position, but found that no university would hire him.

"[9] On the subject of "people the Palestinian society sends to carry out the terrorist attacks," he calls them "serial killers" and "barbarians who want to take our lives".

[9] In the same interview, Morris called Israeli Arabs "a time bomb," claiming that "their slide into complete Palestinization has made them an emissary of the enemy that is among us.

A world in which human life doesn't have the same value as it does in the West, in which freedom, democracy, openness and creativity are alien...Revenge plays a central part in the Arab tribal culture.

He says that according to historical records, approximately 160,000 Arabs remained within the territories of Israel post-1948 and that while many were indeed expelled, a significant number managed to return and retained their status as citizens of the newly established Jewish state.

[19] In July 2019, Morris has sharply criticized the restrictions under the Netanyahu government of access to historical documents related to the 1948 Palestinian Arab exodus, referring to them as "totalitarian.

[26] In an op-ed piece in The New York Times in July 2008, Morris wrote: "Iran's leaders would do well to rethink their gamble and suspend their nuclear program.

[28] Morris reiterated this view in an op-ed in Haaretz in June 2024, writing, "If Israel proves incapable of destroying the Iranian nuclear project using conventional weaponry, then it may not have any option but to resort to its nonconventional capabilities.

"[29][30] In a 2019 interview with Haaretz, Morris took a pessimistic view of Israel's future, arguing that the Palestinians would not compromise and that ultimately "a situation in which we rule an occupied people that has no rights cannot persist in the 21st century, in the modern world".

He claimed that as soon as the Palestinians did have rights, Israel would no longer be a Jewish state, and that it would descend into intercommunal violence with Jews ultimately becoming a persecuted minority and those who could emigrating.

It analyses Mapai and Mapam policy during the exodus, the IDF report of July 1948 on its causes, Yosef Weitz's involvement in the events, and some cases of expulsions that occurred in the fifties.

Morris demolishes misconceptions and provides a detailed account of the war between various factions that year that caused the creation of the modern state of Israel.

[34] The book describes the Ottoman/Turkish destruction of the Armenian, Greek and Assyrian communities by the successive Ottoman, Young Turks' and Atatürk regimes, in which some two million Christians were murdered by their Muslim neighbors.

Shlaim writes that many of Morris's critics cling to the tenets of "Old History", the idea of an Israel born untarnished, a David fighting the Arab Goliath.

He argues that these ideas are simply false, created not by historians but by the participants in the 1948 war, who wrote about the events they had taken part in without the benefit of access to Israeli government archives, which were first opened up in the early 1980s.

[3] Shlomo Ben-Ami, a historian and former Israeli Minister of Foreign Affairs, praised Morris' book The Birth of the Palestinian Refugee Problem Revisited' (2008).

He called it "the single most important work on the thorniest moral and political issue underlying the Israeli-Palestinian conundrum" and suggested it is likely to become "the most definitive study of the first Arab-Israeli war.

"[32] However, Ben-Ami criticised Morris' drawing of an "awkward symmetry" between the Palestinian refugee crisis and the "forced emigration" of Jews from the Arab world.

[32] In his own book Scars of War, Wounds of Peace, Ben-Ami observed that Morris' "thesis about the birth of the Palestine refugee problem being not by design but by the natural logic and evolution of war is not always sustained by the very evidence he himself provides: 'cultured officers ... had turned into base murderers and this not in the heat of battle ... but out of a system of expulsion and destruction; the less Arabs remained, the better; this principle is the political motor for the expulsions and atrocities' [quoting from Morris' major 2004 work 'The Birth of the Palestinian Refugee Problem Revisited']".

He expects his readers to take on trust his assertions that fundamental contradictions exist between published accounts and the underlying documents.....he systematically falsifies evidence.

(Karsh responds that he has an undergraduate degree in modern Middle Eastern history, and Arabic language and literature, and a doctorate in political science and international relations.)

[41] Morris responds that Karsh's article is a "mélange of distortions, half-truths, and plain lies that vividly demonstrates his profound ignorance of both the source material (his piece contains more than fifty footnotes but is based almost entirely on references to and quotations from secondary works, many of them of dubious value) and the history of the Zionist–Arab conflict.

'"[44] Commenting on the Revisited version of Morris'work, Karsh states that in "an implicit acknowledgement of their inaccuracy, Morris has removed some of The Birth's most inaccurate or distorted quotations about transfer.

There are cases in which the overall, final good justifies harsh and cruel acts that are committed in the course of history.Kimmerling describes Morrris's views as "shocking" and says that Morris "has abandoned his historian’s mantle and donned the armor of a Jewish chauvinist who wants the Land of Israel completely cleansed from Arabs" He criticizes the analysis of Morris as misunderstanding the impact of the refugee problem on the current conflict, and the magnitude of an even larger refugee population.

[36] Yoav Gelber has praised Morris's 2008 book on the origins of the 1948 Israeli-Arab war, stating that "In general, however, 1948 is a praiseworthy achievement of research and analysis, the work of a historian unwilling to rest on his already considerable laurels."