2002

In January 2002, the IDF Shayetet 13 naval commandos captured the Karine A, a freighter carrying weapons from Iran towards Israel, believed to be intended for Palestinian militant use against Israel. It was discovered that top officials in the Palestinian Authority were involved in the smuggling, with the Israelis pointing the finger towards Yasser Arafat as also being involved.

Palestinians launched a spate of suicide bombings and attacks against Israel, aimed mostly at civilians. On 3 March, a Palestinian sniper killed 10 Israeli soldiers and settlers and wounded 4 at a checkpoint near Ofra, using an M1 Carbine. He was later arrested and sentenced to life imprisonment. The rate of the attacks increased, and was at its highest in March 2002.

In addition to numerous shooting and grenade attacks, the month saw 15 suicide bombings carried out in Israel — an average of one bombing every two days. The high rate of attacks caused widespread fear throughout Israel and serious disruption of daily life throughout the country. March 2002 became known in Israel as "Black March." On 12 March United Nations Security Council Resolution 1397 was passed, which reaffirmed a Two-state solution and laid the groundwork for a Road map for peace.

On 27 March, the wave of violence culminated with a suicide bombing during a Passover celebration at the Park Hotel in Netanya in which 30 people were killed. The attack became known as the Passover massacre. In total, around 130 Israelis, mostly civilians, were killed in Palestinian attacks during March 2002. On 28 March, Arab leaders, whose constituencies were exposed to detailed television coverage of the violence in the conflict, set out a comprehensive Arab Peace Initiative that was endorsed by Arafat, but virtually ignoring by Israel.

On 29 March, Israel launched Operation Defensive Shield, which lasted until 3 May. The IDF made sweeping incursions throughout the West Bank, and into numerous Palestinian cities. Arafat was put under siege in his Ramallah compound. The UN estimated that 497 Palestinians were killed and 1,447 wounded by the Israeli incursion from 1 March to 7 May. A UN report cleared Israel of allegations of massacre, but criticized it for using excessive force on the civilian population. Israeli forces also arrested 4,258 Palestinians during the operation. Israeli casualties during the operation totaled 30 dead and 127 wounded. The operation culminated with the recapturing of Palestinian Authority controlled areas.

Jenin

Between 2 and 11 April, a siege and fierce fighting took place in the Palestinian refugee camp of the city of Jenin. The camp was targeted during Operation Defensive Shield after Israel determined that it had "served as a launch site for numerous terrorist attacks against both Israeli civilians and Israeli towns and villages in the area." The Jenin battle became a flashpoint for both sides, and saw fierce urban combat as Israeli infantry supported by armor and attack helicopters fought to clear the camp of Palestinian militants. The battle was eventually won by the IDF, after it employed a dozen Caterpillar D9 armored bulldozers to clear Palestinian booby traps, detonate explosive charges, and raze buildings and gun-posts; the bulldozers proved impervious to attacks by Palestinian militants.

During Israeli military operations in the camp, Palestinian sources alleged that a massacre of hundreds of people had taken place. A senior Palestinian Authority official alleged in mid-April that some 500 had been killed. During the fighting in Jenin, Israeli officials had also initially estimated hundreds of Palestinian deaths, but later said they expected the Palestinian toll to reach "45 to 55." In the ensuing controversy, Israel blocked the United Nations from conducting the first-hand inquiry unanimously sought by the Security Council, but the UN nonetheless felt able to dismiss claims of a massacre in its report, which said there had been approximately 52 deaths, criticising both sides for placing Palestinian civilians at risk. Based on their own investigations, Amnesty International and Human Rights Watch charged that some IDF personnel in Jenin had committed war crimes but also confirmed that no massacre had been committed by the IDF. Both human rights organizations called for official inquiries; the IDF disputed the charges.

After the battle, most sources, including the IDF and Palestinian Authority, placed the Palestinian death toll at 52–56; Human Rights Watch documented 52 Palestinian deaths and claimed that it included at least 27 militants and 22 civilians, and an additional 3 Palestinians whose status as militants or civilians could not be ascertained, while the IDF said that 48 militants and 5 civilians had been killed. According to Human Rights Watch, 140 buildings had been destroyed. The IDF reported that 23 Israeli soldiers had been killed and 75 wounded during the battle.

Bethlehem

From 2 April to 10 May, a stand-off developed at the Church of the Nativity in Bethlehem. IDF soldiers surrounded the church while Palestinian civilians, militants, and priests were inside. During the siege, IDF snipers killed 8 militants inside the church and wounded more than 40 people. The stand-off was resolved by the deportation to Europe of 13 Palestinian militants whom the IDF had identified as terrorists, and the IDF ended its 38-day stand-off with the militants inside the church.

2003

Following an Israeli intelligence report stating that Yasir Arafat had paid $20,000 to al-Aqsa Martyrs' Brigades, the United States demanded democratic reforms in the Palestinian Authority, as well the appointment of a prime minister independent of Arafat. On 13 March 2003, following U.S. pressure, Arafat appointed Mahmoud Abbas as Palestinian prime minister.

Following the appointment of Abbas, the U.S. administration promoted the Road map for peace—the Quartet's plan to end the Israeli–Palestinian conflict by disbanding militant organizations, halting settlement activity and establishing a democratic and peaceful Palestinian state. The first phase of the plan demanded that the Palestinian Authority suppress guerrilla and terrorist attacks and confiscate illegal weapons. Unable or unwilling to confront militant organizations and risk civil war, Abbas tried to reach a temporary cease-fire agreement with the militant factions and asked them to halt attacks on Israeli civilians.

On 20 May, Israeli naval commandos intercepted another vessel, the Abu Hassan, on course to the Gaza Strip from Lebanon. It was loaded with rockets, weapons, and ammunition. Eight crew members on board were arrested including a senior Hezbollah member.

On 29 June 2003, a temporary armistice was unilaterally declared by Fatah, Hamas and Islamic Jihad, which declared a ceasefire and halt to all attacks against Israel for a period of three months. Violence decreased somewhat in the following month, but suicide bombings against Israeli civilians continued as well as Israeli operations against militants.

Four Palestinians, three of them militants, were killed in gun battles during an IDF raid of Askar near Nablus involving tanks and armoured personnel carriers (APCs); an Israeli soldier was killed by one of the militants. Nearby Palestinians claimed a squad of Israeli police disguised as Palestinian labourers opened fire on Abbedullah Qawasameh as he left a Hebron mosque. YAMAM, the Israeli counter-terrorism police unit that performed the operation, said Qawasemah opened fire on them as they attempted to arrest him.

On 19 August, Hamas coordinated a suicide attack on a crowded bus in Jerusalem killing 23 Israeli civilians, including 7 children. Hamas claimed it was a retaliation for the killing of five Palestinians (including Hamas leader Abbedullah Qawasameh) earlier in the week. U.S. and Israeli media outlets frequently referred to the bus bombing as shattering the quiet and bringing an end to the ceasefire.

Following the Hamas bus attack, Israeli Defence Forces were ordered to kill or capture all Hamas leaders in Hebron and the Gaza Strip. The plotters of the bus suicide bombing were all captured or killed and Hamas leadership in Hebron was badly damaged by the IDF. Strict curfews were enforced in Nablus, Jenin, and Tulkarem; the Nablus lockdown lasted for over 100 days. In Nazlet 'Issa, over 60 shops were destroyed by Israeli civil administration bulldozers. The Israeli civil administration explained that the shops were demolished because they were built without a permit. Palestinians consider Israeli military curfews and property destruction to constitute collective punishment against innocent Palestinians.

Unable to rule effectively under Arafat, Abbas resigned in September 2003. Ahmed Qurei (Abu Ala) was appointed to replace him. The Israeli government gave up hope for negotiated settlement to the conflict and pursued a unilateral policy of physically separating Israel from Palestinian communities by beginning construction on the Israeli West Bank barrier. Israel claims the barrier is necessary to prevent Palestinian attackers from entering Israeli cities. Palestinians claim the barrier separates Palestinian communities from each other and that the construction plan is a de facto annexation of Palestinian territory.

Following a 4 October suicide bombing in Maxim restaurant, Haifa, which claimed the lives of 21 Israelis, Israel claimed that Syria and Iran sponsored the Islamic Jihad and Hezbollah, and were responsible for the terrorist attack. The day after the Maxim massacre, IAF warplanes bombed an alleged former Palestinian training base at Ain Saheb, Syria, which had been mostly abandoned since the 1980s. Munitions being stored on the site were destroyed, and a civilian guard was injured.

2004
In response to repeated shelling of Israeli communities with Qassam rockets and mortar shells from Gaza, the IDF operated mainly in Rafah – to search and destroy smuggling tunnels used by militants to obtain weapons, ammunition, fugitives, cigarettes, car parts, electrical goods, foreign currency, gold, drugs, and cloth from Egypt. Between September 2000 and May 2004, ninety tunnels connecting Egypt and the Gaza Strip were found and destroyed. Raids in Rafah left many families homeless. Israel's official stance is that their houses were captured by militants and were destroyed during battles with IDF forces. Many of these houses are abandoned due to Israeli incursions and later destroyed. According to Human Rights Watch, over 1,500 houses were destroyed to create a large buffer zone in the city, many "in the absence of military necessity", displacing around sixteen thousand people.

On 2 February 2004, Israeli Prime Minister Ariel Sharon announced his plan to transfer all the Jewish settlers from the Gaza Strip. The Israeli opposition dismissed his announcement as "media spin", but the Israeli Labour Party said it would support such a move. Sharon's right-wing coalition partners National Religious Party and National Union rejected the plan and vowed to quit the government if it were implemented. Yossi Beilin, peace advocate and architect of the Oslo Accords and the Geneva Accord, also rejected the proposed withdrawal plan. He claimed that withdrawing from the Gaza Strip without a peace agreement would reward terror.

Following the declaration of the disengagement plan by Ariel Sharon and as a response to suicide attacks on Erez crossing and Ashdod seaport (10 people were killed), the IDF launched a series of armored raids on the Gaza Strip (mainly Rafah and refugee camps around Gaza), killing about 70 Hamas militants. On 22 March 2004, an Israeli helicopter gunship killed Hamas leader Sheikh Ahmed Yassin, along with his two bodyguards and nine bystanders. On 17 April, after several failed attempts by Hamas to commit suicide bombings and a successful one that killed an Israeli policeman, Yassin's successor, Abdel Aziz al-Rantissi, was killed in an almost identical way, along with a bodyguard and his son Mohammed.

The fighting in Gaza Strip escalated severely in May 2004 after several failed attempts to attack Israeli checkpoints such as Erez crossing and Karni crossing. On 2 May, Palestinian militants attacked and shot dead a pregnant woman and her four young daughters. Amnesty International classified it as a crime against humanity and said it "reiterates its call on all Palestinian armed groups to put an immediate end to the deliberate targeting of Israeli civilians, in Israel and in the Occupied Territories". Additionally, on 11 and 12 May, Palestinian militants destroyed two IDF M-113 APCs, killing 13 soldiers and mutilating their bodies. The IDF launched two raids to recover the bodies, killing 20–40 Palestinians and greatly damaging structures in the Zaitoun neighbourhood in Gaza and in south-west Rafah.

Subsequently, on 18 May the IDF launched Operation Rainbow with a stated aim of striking the militant infrastructure of Rafah, destroying smuggling tunnels, and stopping a shipment of SA-7 missiles and improved anti-tank weapons. A total of 41 Palestinian militants and 12 civilians were killed in the operation, and about 45–56 Palestinian structures were demolished. Israeli tanks shelled hundreds of Palestinian protesters approaching their positions, killing 10. The protesters had disregarded Israeli warnings to turn back. This incident led to a worldwide outcry against the operation.

On 29 September, after a Qassam rocket hit the Israeli town of Sderot and killed two Israeli children, the IDF launched Operation Days of Penitence in the north of the Gaza Strip. The operation's stated aim was to remove the threat of Qassam rockets from Sderot and kill the Hamas militants launching them. The operation ended on 16 October, after having caused widespread destruction and the deaths of over 100 Palestinians, at least 20 of whom were under the age of sixteen. The IDF killed thirteen-year-old Iman Darweesh Al Hams as she strayed into a closed military area; the commander was accused of allegedly firing his automatic weapon at her dead body deliberately to verify the death. The act was investigated by the IDF, but the commander was cleared of all wrongdoing, and more recently, was fully vindicated when a Jerusalem district court found the claim to be libellous, ruled that NIS 300,000 be paid by the journalist and TV company responsible for the report, an additional NIS 80,000 to be paid in legal fees and required the journalist and television company to air a correction. According to Palestinian medics, Israeli forces killed at least 62 militants and 42 other Palestinians believed to be civilians. According to a count performed by Haaretz, 87 militants and 42 civilians were killed. Palestinian refugee camps were heavily damaged by the Israeli assault. The IDF announced that at least 12 Qassam launchings had been thwarted and many terrorists hit during the operation.

On 21 October, the Israeli Air Force killed Adnan al-Ghoul, a senior Hamas bomb maker and the inventor of the Qassam rocket.

On 11 November, Yasser Arafat died in Paris.

Escalation in Gaza began amid the visit of Mahmoud Abbas to Syria in order to achieve a Hudna between Palestinian factions and convince Hamas leadership to halt attacks against Israelis. Hamas vowed to continue the armed struggle, sending numerous Qassam rockets into open fields near Nahal Oz, and hitting a kindergarten in Kfar Darom with an anti-tank missile.

On 9 December five Palestinians weapon smugglers were killed and two were arrested in the border between Rafah and Egypt. Later that day, Jamal Abu Samhadana and two of his bodyguards were injured by a missile strike. In the first Israeli airstrike against militants in weeks, an unmanned Israeli drone plane launched one missile at Abu Samahdna's car as it travelled between Rafah and Khan Younis in the southern Gaza Strip. It was the fourth attempt on Samhadana's life by Israel. Samhadana is one of two leaders of the Popular Resistance Committees and one of the main forces behind the smuggling tunnels. Samhadana is believed to be responsible for the blast against an American diplomatic convoy in Gaza that killed three Americans.

On 10 December, in response to Hamas firing mortar rounds into the Neveh Dekalim settlement in the Gaza Strip and wounding four Israelis (including an 8-year-old boy), Israeli soldiers fired at the Khan Younis refugee camp (the origin of the mortars) killing a seven-year-old girl. An IDF source confirmed troops opened fire at Khan Younis, but said they aimed at Hamas mortar crews.

The largest attack since the death of Yasser Arafat claimed the lives of five Israeli soldiers on 12 December, wounding ten others. Approximately 1.5 tons of explosives were detonated in a tunnel under an Israeli military-controlled border crossing on the Egyptian border with Gaza near Rafah, collapsing several structures and damaging others. The explosion destroyed part of the outpost and killed three soldiers. Two Palestinian militants then penetrated the outpost and killed two other Israeli soldiers with gunfire. It is believed that Hamas and a new Fatah faction, the "Fatah Hawks", conducted the highly organised and coordinated attack. A spokesman, "Abu Majad", claimed responsibility for the attack in the name of the Fatah Hawks claiming it was in retaliation for "the assassination" of Yasser Arafat, charging he was poisoned by Israel.

2005
Palestinian presidential elections were held on 9 January, and Mahmoud Abbas (Abu Mazen) was elected as the president of the PA. His platform was of a peaceful negotiation with Israel and non-violence to achieve Palestinian objectives. Although Abbas called on militants to halt attacks against Israel, he promised them protection from Israeli incursions and did not advocate disarmament by force.

Violence continued in the Gaza Strip, and Ariel Sharon froze all diplomatic and security contacts with the Palestinian National Authority. Spokesman Assaf Shariv declared that "Israel informed international leaders today that there will be no meetings with Abbas until he makes a real effort to stop the terror." The freezing of contacts came less than one week after Mahmoud Abbas was elected, and the day before his inauguration. Palestinian negotiator Saeb Erekat, confirming the news, declared "You cannot hold Mahmoud Abbas accountable when he hasn't even been inaugurated yet."

Following international pressure and Israeli threat of wide military operation in the Gaza Strip, Abbas ordered Palestinian police to deploy in the northern Gaza Strip to prevent Qassam rocket and mortar shelling over Israeli settlement. Although attacks on Israelis did not stop completely, they decreased sharply. On 8 February 2005, at the Sharm el-Sheikh Summit of 2005, Sharon and Abbas declared a mutual truce between Israel and the Palestinian National Authority. They shook hands at a four-way summit that also included Jordan and Egypt at Sharm al-Sheikh. However, Hamas and Islamic Jihad said the truce is not binding for their members. Israel has not withdrawn its demand to dismantle terrorist infrastructure before moving ahead in the Road map for peace.

Many warned that truce is fragile, and progress must be done slowly while observing that the truce and quiet are kept. On 9–10 February night, a barrage of 25–50 Qassam rockets and mortar shells hit Neve Dekalim settlement, and another barrage hit at noon. Hamas said it was in retaliation for an attack in which one Palestinian was killed near an Israeli settlement. As a response to the mortar attack, Abbas ordered the Palestinian security forces to stop such attacks in the future. He also fired senior commanders in the Palestinian security apparatus. On 10 February, Israeli security forces arrested Maharan Omar Shucat Abu Hamis, a Palestinian resident of Nablus, who was about to launch a bus suicide attack in the French Hill in Jerusalem.

On 13 February 2005, Abbas entered into talks with the leaders of the Islamic Jihad and the Hamas, for them to rally behind him and respect the truce. Ismail Haniyah, a senior leader of the group Hamas said that "its position regarding calm will continue unchanged and Israel will bear responsibility for any new violation or aggression."

In the middle of June, Palestinian factions intensified bombardment over the city of Sderot with improvised Qassam rockets. Palestinian attacks resulted in 2 Palestinians and 1 Chinese civilian killed by a Qassam, and 2 Israelis were killed. The wave of attacks lessened support for the disengagement plan among the Israeli public. Attacks on Israel by the Islamic Jihad and the al-Aqsa Martyrs' Brigades increased in July, and on 12 July, a suicide bombing hit the coastal city of Netanya, killing 5 civilians. On 14 July, Hamas started to shell Israeli settlements inside and outside the Gaza Strip with dozens of Qassam rockets, killing an Israeli woman. On 15 July, Israel resumed its "targeted killing" policy, killing 7 Hamas militants and bombing about 4 Hamas facilities. The continuation of shelling rockets over Israeli settlements, and street battles between Hamas militants and Palestinian policemen, threatened to shatter the truce agreed in the Sharm el-Sheikh Summit of 2005. The Israeli Defence Force also started to build up armored forces around the Gaza Strip in response to the shelling.

End of the Intifada
The ending date of the Second Intifada is disputed, as there was no definite event that brought it to an end. The general views is that it ended in 2005, while some sources include events and statistic for the intifada as far as 2007.

 Some commentators such as Sever Plocker consider the intifada to have ended in late 2004. With the sickness and then death of Yasser Arafat in November 2004, the Palestinians lost their internationally recognised leader of the previous three decades, after which the intifada lost momentum and lead to internal fighting between Palestinian factions (most notably the Fatah–Hamas conflict), as well as conflict within Fatah itself.
 Israel's unilateral disengagement from the Gaza Strip, announced in June 2004 and completed in August 2005, is also cited, for instance by Ramzy Baroud, as signalling the end of the intifada.
 Some consider 8 February 2005 to be the official end of the Second Intifada, although sporadic violence still continued outside PA control or condonation. On that day, Abbas and Sharon met at the Sharm el-Sheikh Summit where they vowed to end attacks on each other. In addition, Sharon agreeing to release 900 Palestinian prisoners and withdraw from West Bank towns. Hamas and Palestinian Islamic Jihad (PIJ) refused to be parties to the agreement, arguing the cease-fire was the position of the PA only. Five days later Abbas reached agreement with the two dissenting organizations to commit to the truce with the proviso that Israeli violation would be met with retaliation.

Schachter addressed the difficulties in deciding when this intifada ended. He reasoned that suicide bombing was the best criterion, being arguably the most important element of second intifada-related violence, and that according to this criterion the intifada ended during 2005.

第2次インティファーダの原因
第2次インティファーダは、リクード所属の首相候補であるアリエル・シャロンが神殿の丘あるいはハラム・アッシャリーフとして知られるユダヤ教とイスラームの聖域に1000人以上の護衛とともに訪問したことがきっかけとなり、2000年9月28日に勃発した。訪問した際、シャロンは"the Temple Mount is in our hands and will remain in our hands. It is the holiest site in Judaism and it is the right of every Jew to visit the Temple Mount."と述べている。

この訪問は、パレスチナ側に非常に挑発的な行動と受け止められ、パレスチナのデモ隊は警察に対して投石したが、イスラエル軍にゴム弾や催涙ガスで追い払われ、その地でパレスチナの暴動が発生し、イスラエル軍と民衆が衝突する結果となった。