Gaza’s hospitals have emerged as a focal point in Israel’s war with Hamas, with each side citing how the other has pulled the facilities into the conflict as proof of the enemy’s disregard for the safety of civilians.

In four months of war, Israeli troops have entered several hospitals, including the Qatari Hospital, Kamal Adwan Hospital and Al-Rantisi Specialized Hospital for Children, to search for weapons and fighters. But Al-Shifa Hospital has taken on particular significance because it is Gaza’s largest medical facility, and because of Israel’s high-profile claims that Hamas leaders operated a command-and-control center beneath it. Hamas and the hospital’s staff, meanwhile, insisted it was only a medical center.

Al-Shifa’s value as a military target was not immediately clear in the days after the Nov. 15 raid, even after the Israeli military released the tunnel video that was used to create the 3-D model seen here.

But evidence examined by The New York Times suggests Hamas used the hospital for cover, stored weapons inside it and maintained a hardened tunnel beneath the complex that was supplied with water, power and air-conditioning.

Classified Israeli intelligence documents, obtained and reviewed by The Times, indicate that the tunnel is at least 700 feet long, twice as long as the military revealed publicly, and that it extends beyond the hospital and likely connects to Hamas’s larger underground network.

According to classified images reviewed by The Times, Israeli soldiers found underground bunkers, living quarters and a room that appeared to be wired for computers and communications equipment along a part of the tunnel beyond the hospital — chambers that were not visible in the video released by the Israeli military.

The Israeli military, however, has struggled to prove that Hamas maintained a command-and-control center under the facility. Critics of the Israeli military say the evidence does not support its early claims, noting that it had distributed material before the raid showing five underground complexes and also had said the tunnel network could be reached from wards inside a hospital building. Israel has publicly revealed the existence of only one tunnel entrance on the grounds of the hospital, at the shack outside its main buildings.

The Israeli military says that it moved carefully because the tunnel was booby-trapped and ran out of time to investigate before it destroyed the tunnel and withdrew from the hospital. Israeli and Qatari officials, speaking on condition of anonymity, said Israel had to leave the hospital to comply with the terms of a temporary ceasefire in late November.

American officials have said their own intelligence backs up the Israeli case, including evidence that Hamas used Al-Shifa to hold at least a few hostages. American intelligence also indicates that Hamas fighters evacuated the complex days before Israeli forces moved into Al-Shifa, destroying documents and electronics as they left.

Hospitals are protected under international law, even if they provide medical care for combatants, but their use for other acts that are “harmful to the enemy” can make them legitimate targets for military action. But any action must weigh the expected military advantage against the expected harm to civilians.

Al-Shifa, Israeli officials have argued, is an example of Hamas’s willingness to use hospitals as cover and turn civilians into human shields. But critics say it is also an example of the toll on civilians when Israeli forces surround and raid hospitals to pursue Hamas fighters or rescue hostages, operations that can cut off doctors from fuel and supplies and residents from urgently needed medical care.

Five premature babies died at Al-Shifa before the raid “due to lack of electricity and fuel,” according to the U.N. Office for the Coordination of Humanitarian Affairs, which helped organize the evacuation of 31 other infants.

“We all know that the health care system is or has collapsed,” Lynn Hastings, the U.N.’s humanitarian coordinator for Gaza, has told reporters.

Israel launched its war in Gaza after the Hamas-led attack on Oct. 7, in which at least 1,200 people were killed and more than 200 were taken hostage. Since the start of the war, more than 28,000 people have been killed in Gaza, according to health officials there.

In the face of international opprobrium over its raids on hospitals, Israel has publicized evidence that it says shows that Hamas hid fighters among the ill and injured, and held hostages in the facilities. The Israeli military said that before entering Al-Shifa, it warned the buildings’ occupants, opened evacuation routes and sent Arabic-speaking medical teams along with the soldiers.

Hamas and Gazan health officials say the hospitals have served only as medical facilities. But beyond accusing the Israeli military of planting evidence at hospitals, Hamas and Gazan officials have not directly refuted the evidence presented by Israel.

The Israeli military said it apprehended dozens of “terror operatives” at Kamal Adwan Hospital in December, and released videos, at the time, of men carrying weapons. A spokesman for the health ministry in Gaza said that Israeli forces had asked the hospital’s administrators to hand over the weapons of its security guards.

After the raid on the Qatari Hospital, the commonly used name for the Sheikh Hamad bin Khalifa Al Thani Hospital for Rehabilitation and Prosthetics, the Israeli military showed a video on Nov. 5 of what it said was the entrance to “a tunnel that was being used for terror infrastructures” on the hospital’s grounds.

But the video appears to show something else: a water storage area built in 2016, when the hospital was constructed, according to engineering plans and images from the hospital’s construction reviewed by The Times.

The Israeli military declined to provide additional imagery to support its assertion that this was a tunnel entryway or part of a tunnel complex.

Just before the Al-Shifa raid, Israeli forces entered Al-Rantisi hospital, on Nov. 13, soon after its remaining patients and staff had left. Within days, the military released two videos that showed weapons and explosives it said it found there, and a room where it said hostages had been kept. The health ministry in Gaza disputed the assertions made in the videos and said the weapons were planted.

One of the videos released by Israel showed troops rushing into the hospital and appearing to find explosives, weapons and the hostage room. In the other, Rear Adm. Daniel Hagari, chief spokesman for the Israeli military, showed off guns, explosives and other weapons that he said were found in the basement of the hospital.

The video included footage of a piece of paper taped to a wall in the hospital’s basement. Admiral Hagari said the paper — a grid with Arabic words and numbers within each square — could be a schedule for guarding hostages “where every terrorist writes his name.”

The Gazan health ministry said it was nothing more than a work schedule. But the calendar begins on Oct. 7, the day of the Hamas terrorist attack on Israel, and an Arabic title written at the top uses the militants’ name for the assault: “Al Aqsa Flood Battle, 7/10/2023.”

Given its size and history, taking control of Al-Shifa was always a more important goal for the Israeli military than the other smaller facilities.

There is substantial independent evidence that Hamas constructed a vast tunnel network across Gaza. Senior Israeli defense officials, who spoke on the condition of anonymity to discuss intelligence matters, estimate the network is between 350 and 450 miles — extraordinary figures for a territory that at its longest point is only 25 miles. The officials estimate there are thousands of entrances to the network.

There is also established documentation that Hamas used Al-Shifa before the war to mask some of its activities. During Israel’s three-week war with Hamas in 2008, armed Hamas fighters in civilian clothing were seen roaming Al-Shifa’s corridors and killing an Israeli collaborator, according to a Times correspondent reporting in Gaza at the time. Six years later, during the next round of fighting, the militants routinely held news conferences at the hospital and used it as a safe meeting place for Hamas officials to speak with journalists.

After that war, Amnesty International reported that Hamas had used abandoned areas of Al-Shifa, “including the outpatients’ clinic area, to detain, interrogate, torture and otherwise ill-treat suspects, even as other parts of the hospital continued to function as a medical center.”

Israel’s critics, though, countered with statements made at the time by two Norwegian doctors, who described themselves as pro-Palestinian activists and had worked in Gaza during the 2014 war. They insisted that they saw no Hamas presence at Al-Shifa.

Israel has also released video footage, taken by the hospital’s own security cameras, which it says shows two hostages being brought to Al-Shifa shortly after being abducted in the Oct. 7 attack.

The Al-Shifa tunnel was discovered by following ducts that ran underground from air-conditioning units that were powered by the hospital’s electricity supply and mounted on one of its buildings, officials said. Israeli soldiers also found evidence that the hospital’s water supply was being fed to the tunnel.

The Israeli military has also displayed weapons and other equipment it said were found inside Al-Shifa, including grenades placed near an MRI machine. Among the cache presented to journalists were belongings that Israeli officials said had been taken from hostages, including a bag emblazoned with the name Be’eri, a kibbutz attacked by Hamas.

The military also said it found weapons in Al-Shifa’s parking lot, and a Toyota vehicle identical to those used in the Oct. 7 attack and loaded with the same equipment that militants carried during the raid, including guns and rocket-propelled grenades. Israeli officials speculated that it was a spare vehicle not used in the attack.

Some of what the Israeli military has shown so far does not wholly match the description of a terrorist headquarters that it offered ahead of its ground invasion of Gaza on Oct. 27.

Underneath Al-Shifa, the Israeli military wrote in a lengthy post on its website, “lies a labyrinth of tunnels and underground compounds used by Hamas’s leaders to direct terrorist activities and rocket fire and to manufacture and store a variety of weapons and ammunition.”

There may no longer be a way to directly assess that claim. Israeli forces remained at Al-Shifa for a little more than a week.

Hours before Israeli forces left the hospital on Nov. 24, soldiers lined the tunnel with explosives and destroyed it in a blast that sent plumes of smoke high into the air and rocked buildings on the ground above.