The Roadmap was offered for acceptance "as it is", without room for adaptations. The Government statement of 25 May 2003, however, made clear that Israel regarded its reservations part of the Roadmap:

"The Government of Israel affirms the Prime Minister's announcement, and resolves that all of Israel's comments, as addressed in the Administration's statement, will be implemented in full during the implementation phase of the Roadmap."

Furthermore, the Government definitively ruled out the right of return:

"The Government of Israel further clarifies that, both during and subsequent to the political process, the resolution of the issue of the refugees will not include their entry into or settlement within the State of Israel."

A U.S. official, however, said that U.S. commitment did not mean that all of Israel's demands would be met. Abbas called the Israeli reservations to the map "not part of the map and ... not relevant to its implementation, and ... not acceptable to the Palestinians."

The first step on the Roadmap was the appointment of the first-ever Palestinian prime minister Mahmoud Abbas (also known as Abu Mazen), by Palestinian leader Yasser Arafat. The United States and Israel demanded that Arafat be neutralized or sidelined in the Roadmap process, claiming that he had not done enough to stop Palestinian attacks against Israelis while in charge. The United States refused to release the Roadmap until a Palestinian prime minister was in place. Abbas was appointed on 19 March 2003, clearing the way for the release of the Roadmap's details on 30 April 2003.

The publication of the Roadmap could not stop the violence of the Second Intifada. Hamas rejected it, saying that "Abu Mazen is betraying the Palestinian people's struggle and jihad in order to appease the USA and to avoid angering Israel". From 1 to 17 May 2003, 43 Palestinian civilians were killed; from 5 to 17 May, 4 Israeli civilians. After a suicide attack on 18 May, which killed 6 Israelis, the army carried out 35 punitive demolitions of Palestinian homes.On 27 May 2003, Israeli Prime Minister Ariel Sharon stated that the "occupation" of Palestinian territories was "a terrible thing for Israel and for the Palestinians" and "can't continue endlessly." Sharon's phraseology prompted shock from many in Israel, leading to a clarification that by "occupation," Sharon meant control of millions of Palestinian lives rather than actual physical occupation of land.The Route 60 ambush took place on June 20, as Secretary of State Colin Powell was in Jerusalem engaging in peace negotiations.

President Bush visited the Middle East from 2 to 4 June 2003 for two summits as part of a seven-day overseas trip through Europe and Russia in an attempt to push the Roadmap. On 2 June, Israel freed about 100 Palestinian prisoners before the first summit in Egypt as a sign of goodwill. The list consisted largely of administrative detainees who were due to be released. Subsequent prisoner releases involved members of Hamas and Islamic Jihad, but the government insisted that those slated for release did not have Israeli "blood on their hands." In Egypt on 3 June, President Bush met with the leaders of Egypt, Saudi Arabia, Jordan and Bahrain, and with Prime Minister Abbas. The Arab leaders announced their support for the Roadmap and promised to work on cutting off funding to terrorist groups. On 4 June, Bush headed to Jordan to meet directly with Ariel Sharon and Mahmoud Abbas.

After Bush left the region violence resumed, threatening to derail the Roadmap plan.

On 29 June 2003, a tentative unilateral cease-fire ("hudna" in Arabic) was declared by the Palestinian Authority and four major Palestinian groups. Palestinian Islamic Jihad and Hamas announced a joint three-month cease-fire, while Yasser Arafat's Fatah faction declared a six-month truce. The cease-fire was later joined by the Democratic Front for the Liberation of Palestine. One condition of maintaining the truce was a demand for the release of prisoners from Israeli jails, which was not part of the Roadmap process. This coincided with a visit to the region by United States National Security Advisor Condoleezza Rice.

On 1 July 2003, in Jerusalem, Sharon and Abbas held a first-ever ceremonial opening to peace talks, televised live in both Arabic and Hebrew. Both leaders said the violence had gone on too long and that they were committed to the Roadmap for peace. On 2 July, Israeli troops pulled out of Bethlehem and transferred control to Palestinian security forces. The plan required that Palestinian police take over from withdrawing Israeli forces and stop any anti-Israeli militant attacks. At the same time, the U.S. announced a $30 million aid package to the Palestinian Authority to help rebuild infrastructure destroyed by Israeli incursions.

The hudna quickly collapsed. On 3 July, the IDF killed 2 civilians. In an IDF operation to arrest Hamas members, gunfight broke out in which an Israeli soldier and two alleged Hamas militants were killed. A new cycle of violence happened. Hamas responded with a suicide bombing on 12 August, killing one Israeli civilian. Fatah claimed responsibility for a second suicide bombing on 12 August, killing another Israeli citizen. Despite this de facto violation of the hudna, Hamas stated that the cease-fire would continue.

Hostilities then escalated. The Israeli army killed Islamic Jihad's Muhammad Seeder on 14 August 2003; the Jerusalem bus 2 massacre by Hamas and Islamic Jihad on 19 August, killed 23 and wounded 136 people. Israel reacted causing large-scale destruction to Palestinian population centres. On 21 August, Israel assassinated Hamas' political leader Ismail Abu Shanab. Shanab, who supported a two-state solution, strongly opposed suicide bombings and tried to uphold the ceasefire, was regarded as one of Hamas's more moderate and pragmatic leaders. Along with Shanab, three other civilians (his two bodyguards and a 74-year-old man) were killed. The following days it continued with a range of further Israeli killing-attacks. The assassinations of Seeder and Shanab resulted in Hamas calling off the ceasefire with Israel. International criticism of Israel increased because Israel was widely believed to be unwilling to respect the truce.

In November 2003, the United Nations Security Council endorsed the Roadmap in United Nations Security Council Resolution 1515 which called for an end to all violence including "terrorism, provocation, incitement and destruction". By the end of 2003, the Palestinian Authority had not prevented Palestinian terrorism, and Israel had neither withdrawn from Palestinian areas occupied since 28 September 2000, nor frozen settlement expansion. Thus the requirements of Phase I of the Roadmap were not fulfilled, and the Roadmap has not continued further. It eventually reached deadlock.

On 14 April 2004, Prime Minister Ariel Sharon wrote a letter to US President George W. Bush, in which he reconfirmed his commitment to the Roadmap. He also accused the Palestinian Authority of not carrying out its part of the responsibilities under the Roadmap. Stating that "there exists no Palestinian partner with whom to advance peacefully toward a settlement", Sharon announced his unilateral disengagement plan (Israeli withdrawal from Gaza), which meant the removal of all Israeli settlements from the Gaza Strip and four settlements in the West Bank. The plan was already suggested by him on 18 December 2003 at the Fourth Herzliya Conference.Although not undertaken under the Roadmap, Sharon declared this unilateral step not inconsistent with it. President Bush gave his support to the plan, calling it "a bold and historic initiative that can make an important contribution to peace".

Until 2004, the official U.S. position had been that Israel, in principle, should return to the 1949 armistice lines (the Green Line) and that changes to these lines must be mutually agreed to in final-status negotiations. Israel's ongoing settlement activities were criticised, because they prejudiced final-status negotiations.

In his answer on the 14 April letter from Ariel Sharon, Bush took some distance from this principle. He said "In light of new realities on the ground, including already existing major Israeli population centers, it is unrealistic that the outcome of final status negotiations will be a full and complete return to the armistice lines of 1949 .... It is realistic to expect that any final status agreement will only be achieved on the basis of mutually agreed changes 'that reflect these realities'."Regarding the Palestinian refugees Bush said that "It seems clear that an agreed, just, fair and realistic framework for a solution to the Palestinian refugee issue as part of any final status agreement will need to be found through the establishment of a Palestinian state and the settling of Palestinian refugees there rather than in Israel."The letter was widely seen as a triumph for Sharon, since Bush seemed to accept Israel's policy of facts on the ground, the view that the passage of time and new realities (Israeli settlements in the West Bank) obviated Israel's obligation to withdraw more or less to the 1967 lines in return for peace, recognition and security.In a 26 May 2005 joint press conference with Palestinian leader Mahmoud Abbas in the White House Rose Garden, President Bush said: "Any final status agreement must be reached between the two parties, and changes to the 1949 armistice lines must be mutually agreed to. A viable two-state solution must ensure contiguity of the West Bank, and a state of scattered territories will not work. There must also be meaningful linkages between the West Bank and Gaza. This is the position of the United States today, it will be the position of the United States at the time of final status negotiations."This statement was widely seen as a triumph for Abbas, as many commentators view it as contradictory to his 14 April 2004 letter. The Bush administration made no attempts to clarify any perceived discrepancies between the two statements.

While the Palestinians persisted in violent attacks against Israelis, Israel executed major military operations in Gaza. In 2004, most Israeli civilians were killed in 6 bomb attacks inside Israel. The Israeli army invaded and besieged southern Gaza in May in Operation Rainbow, invaded and besieged Beit Hanoun in northern Gaza in the summer in a 37 days long raid, and invaded northern Gaza again from 29 September to 16 October in Operation Days of Penitence.

The Roadmap was based on president Bush's idea that Palestinian terror was the primary obstacle for an Israeli–Palestinian peace agreement, that the Palestinian authorities (PA) were encouraging terrorism, and that the dismantling of the current Palestinian leadership was a prerequisite for a Palestinian state. In his speech of 24 June 2002, Bush said:

"Peace requires a new and different Palestinian leadership, so that a Palestinian state can be born. I call on the Palestinian people to elect new leaders, leaders not compromised by terror." ... "And when the Palestinian people have new leaders, new institutions and new security arrangements with their neighbors, the United States of America will support the creation of a Palestinian state whose borders and certain aspects of its sovereignty will be provisional until resolved as part of a final settlement in the Middle East." ... "Today, Palestinian authorities are encouraging, not opposing, terrorism." ... "The Palestinian Authority has rejected your [the Israeli] offer at hand, and trafficked with terrorists."

Israel agreed. It wanted to expel Arafat, but the US opposed. Instead it was suggested to create the post of Prime Minister. In October 2003, the Government declared that "Arafat is the main obstacle for any progress in the Middle East peace process." Prime Minister Ariel Sharon said there is no hope for a political settlement "as long as [Arafat] is around.", but he considered expelling Arafat not good for Israel.

Although President Arafat had undertaken significant reform steps since May 2002, the process stalled from March 2003 due to both Israeli measures and internal political factors. In March 2003, President Arafat nominated Mahmoud Abbas for the post of the first Prime Minister. On 29 April, the Palestinian Parliament approved the appointment of the PM and his new Government. However, a struggle for power between Abbas and Arafat as well as members of the old clique paralysed the new government. Abbas was in a weak position, due to his failing to counter the Israelis, who refused to release prisoners and continued with the occupation of Palestinian cities, settlement activities, assassinations and incursions, and the maintenance of checkpoints. Abbas resigned in September 2003. Also under his successor Ahmed Qurei (Abu Alaa), the needed reform did not appear. An international task force concluded that only general elections could transform the political system, which, however, was impossible under the continued Israeli occupation. After Arafat's death in November 2004, Abbas was elected as the second President of the Palestinian Authority.

The PA was created by the Oslo Accords and set out in detail. The PA was committed to combat Palestinian terror. Yet, its Security Forces were banned from Area C, some 60% of the West Bank, where Israel has exclusive responsibility for security control. Moreover, they were not able to move freely between all parts of the Palestinian controlled areas, which were splintered into more than 160 enclaves within Area C. Nevertheless, Israel held the PA, notably President Arafat, responsible for terrorist attacks committed by militant groups who were not affiliated with him. After two suicide bombings in Israel and Jerusalem executed by Hamas members, the Israeli security Cabinet decided on 11 September 2003 that "Israel will act to remove this obstacle [Arafat] in the manner, at the time, and in the ways that will be decided on separately".Israel on principle refused to accept cease-fires with militant groups, because "Israel deals only with the Palestinian Authority" and "The Israelis don't deal with these terrorist organizations", while advancing its policy of targeted killing. Instead, Israel reacted on terrorist attacks by attacking the PA's Security Forces and its offices.When the Second Intifada began, Israel started with the systematic destruction of security service's offices until 90% of them were destroyed by 2003, and about three-quarters of the national security officers were locked up in Israeli detention camps, others were killed. Israeli attacks were mainly concentrated on Palestinian security forces, even though Hamas was responsible for a majority of the bombings and shootings. The siege of Arafat's compound, which started in March 2002 during Operation Defensive Shield was maintained in 2003 and 2004, until Arafat died in a mysterious way.

With the destruction of hundreds of PA offices, like the Education Ministry, the Higher Education Ministry and the Health Ministry, along with equipment, computers and dossiers, the IDF wiped out the public data banks, according to Amira Hass apparently to destroy Palestinian civil institutions, sabotaging for years to come the Palestinian goal for independence.