Gaza Conflict: IDF’s Rafah Operations Amid Fragile Ceasefire and Deepening Humanitarian Crisis 

Despite a ceasefire agreement that has brought tentative calm to the region, the conflict in Gaza remains perilously fragile, as evidenced by recent IDF operations that killed five Palestinian militants in Rafah and the simultaneous, Red Cross-facilitated return of a hostage’s remains—contradictory events that highlight both fragile cooperation and persistent violations, all while a severe humanitarian crisis deepens amid winter storms, destroyed infrastructure, and obstructed aid, with regional diplomats from Turkey, Egypt, and Qatar scrambling to uphold the truce and transition to a more stable peace despite the ongoing threat of escalation.

Gaza Conflict: IDF’s Rafah Operations Amid Fragile Ceasefire and Deepening Humanitarian Crisis 

More than 72,500 lives have been lost in a conflict that has left international agreements hanging by a thread and a population struggling for survival. 

The Israel Defense Forces reported killing five Palestinian militants in Gaza’s Rafah this week, in a operation that underscores the ongoing tensions despite a ceasefire agreement that has brought tentative calm to the region. The incident occurred as Israeli authorities confirmed the return of a hostage’s remains through a Red Cross-mediated transfer, highlighting both the fragile cooperation between warring parties and the persistent violations that threaten to unravel the tenuous peace. 

The operations in Rafah, which the IDF says targeted militants hiding underground, reveal the complex challenges facing the ceasefire implemented in January 2025. As mediators from Turkey, Egypt, and Qatar work to solidify the agreement, the people of Gaza face a deepening humanitarian crisis exacerbated by recent winter storms that have flooded makeshift camps and created new threats of disease among displaced populations. 

1. Recent Developments in the Conflict

The IDF confirmed that its forces killed five armed militants in eastern Rafah who had been identified earlier Tuesday hiding underground. This operation demonstrates the continued military activity persisting despite the ceasefire formally remaining in effect . According to reports, Israeli troops have eliminated more than 20 terrorists in Rafah in the past week alone, indicating significant ongoing operations against militant cells in the area. 

In a separate incident along the “Yellow Line” demarcating IDF-controlled territory in northern Gaza, Israeli soldiers killed another individual who had crossed and allegedly “posed an immediate threat” to them. These incidents illustrate how tense standoffs and violent confrontations continue to occur despite the broader ceasefire framework. 

In a significant development, Israeli authorities took possession of remains believed to be those of a deceased hostage. The body was transported via Red Cross convoy to Israel’s National Institute of Forensic Medicine for formal identification. This transfer represents one of the painful but necessary exchanges contemplated under the ceasefire agreement, though disagreements persist about the implementation of these provisions . 

2. The Strategic Significance of Rafah

Rafah has emerged as a critical flashpoint in the ongoing conflict. Located along Gaza’s border with Egypt, this southern city has served as both a humanitarian lifeline and a military battleground. The IDF maintains control over Rafah and other areas along the “Yellow Line” as stipulated in the ceasefire agreement, a strategic positioning that allows Israel to monitor and intercept potential security threats while maintaining influence over border crossings . 

The city’s underground infrastructure has become a particular focus of military operations. In early November, reports indicated that up to 200 Hamas fighters were hiding in several tunnels beneath Rafah, representing the remnants of the Hamas Rafah Brigade that Israeli forces have confronted repeatedly throughout the two-year conflict . These tunnel networks pose significant security challenges for the IDF, as they allow militants to move undetected, store weapons, and launch surprise attacks. 

The persistent violence in Rafah illustrates what many analysts have feared: that the ceasefire agreement has failed to fully dismantle militant networks or address the underlying security concerns that precipitated the conflict. Despite the formal truce, the situation in Rafah demonstrates how isolated clashes can quickly escalate, threatening to unravel the broader peace process. 

3. The Role of Palestinian Islamic Jihad

The Palestinian Islamic Jihad (PIJ) has played a significant role in the current conflict, often operating in coordination with Hamas while maintaining its own organizational structure and strategic objectives. Designated as a foreign terrorist organization by the U.S. State Department in 1997, PIJ represents the second-largest militant group in Gaza after Hamas . 

PIJ’s military wing, the al-Quds Brigades, has developed substantial capabilities including small arms, mortars, rockets, MANPADS, armed unmanned aircraft systems, antitank guided missiles, and improvised explosive devices. The group draws inspiration from the Iranian Revolution and receives material support from Iran and Lebanese Hezbollah, creating a regional dynamic that extends far beyond Gaza’s borders . 

Table: Palestinian Islamic Jihad’s Notable Operations 

The group’s leadership structure includes Ziyad al-Nakhalah as Secretary General, Muhammad al-Hindi as Deputy Secretary General, and Akram al-‘Ajuri as commander of the al-Quds Brigades. With approximately 4,000 fighters in its ranks, PIJ represents a significant military force that continues to operate despite Israeli operations that have “partially degraded” its capabilities . 

4. The Ceasefire Agreement: Context and Challenges

The current ceasefire stems from the three-phase agreement finalized on January 15, 2025, after months of intense negotiations mediated by Egypt, Qatar, and the United States. This agreement implemented the first stage of what would become former President Donald Trump’s 20-point Gaza peace plan, which envisioned an international force eventually replacing Israeli troops in Gaza . 

The agreement established a 42-day truce for each of its three phases, beginning with the release of 33 Israeli hostages meeting specific humanitarian criteria (women, children, injured, and elderly) in exchange for 30-50 Palestinian prisoners per hostage. Subsequent phases addressed permanent ceasefire arrangements, additional hostage releases, and the return of deceased hostages’ remains . 

Despite this carefully structured framework, the implementation has faced significant challenges. Hamas has struggled to locate and return all deceased hostages, citing that Israeli forces had “altered the terrain of Gaza” and that “some of those who buried the bodies have been martyred or no longer remember where they buried them” . Israel has rejected these explanations, insisting Hamas knows the locations of all bodies. 

The situation escalated when Hamas handed over a coffin containing remains that forensic tests revealed belonged to Ofir Tzarfati, an Israeli hostage whose body had already been recovered by Israeli forces in late 2023. Israel condemned this as a “clear violation” of the ceasefire agreement, while Hamas rejected what it called “baseless allegations” and accused Israel of seeking “to fabricate false pretexts in preparation for taking new aggressive steps” . 

5. The Deepening Humanitarian Crisis

Behind the military and diplomatic maneuvers lies a devastating humanitarian catastrophe that continues to worsen despite the ceasefire. The Gaza Ministry of Health reported in late November 2024 that more than 44,000 people had been killed and 104,000 wounded since hostilities escalated on October 7, 2023 . These figures do not include those who have died from “preventable disease, malnutrition and other consequences of the war,” suggesting the actual death toll may be significantly higher . 

5.1. Health System Collapse 

Gaza’s healthcare infrastructure has been pushed to the brink of total collapse. As of November 2025, “not a single hospital in Gaza is fully functional,” with only 18 out of 36 hospitals partially operational . The collapse of the healthcare system has had particularly severe consequences for vulnerable populations, including an estimated 50,000 pregnant women and girls who have been deprived of access to adequate care . 

UN agencies report that more than 16,500 patients require urgent medical evacuation outside Gaza for conditions that cannot be treated within the territory . However, Israel has severely restricted medical evacuations, allowing only approximately 320 critical patients to leave Gaza between May and November 2025 . 

5.2. Aid Access and Basic Necessities 

The delivery of humanitarian aid continues to face systematic obstacles. On a single day in November 2025, the UN and its partners coordinated eight planned humanitarian movements inside Gaza with Israeli authorities. Of these, only one movement was facilitated, while the remaining seven were “impeded, denied or cancelled” . This pattern of obstruction has created catastrophic shortages of food, clean water, and medical supplies across the territory. 

The water crisis has been particularly severe, with people having access to less than 5 liters of water per day on average—just one-third of the WHO’s minimum standard for survival. This deprivation has contributed to a public health disaster, with cases of diarrhea among children under five increasing from 2,000 per month before October 2023 to 71,000 as of January 2024 . 

Table: Impact of the Conflict on Gaza’s Civilian Infrastructure 

The educational system has suffered near-total devastation, with 87% of all schools and all universities in Gaza damaged or destroyed . Despite these challenges, the UN agency assisting Palestine refugees (UNRWA) has established nearly 350 temporary learning spaces in 64 shelters, providing in-person education for more than 47,000 children . 

6. Regional Diplomacy and International Response

The ceasefire agreement has prompted intensive diplomatic efforts from regional and international actors seeking to stabilize the situation and prevent a return to full-scale conflict. On Tuesday, Turkey’s intelligence chief met with his Egyptian counterpart and Qatar’s foreign minister in Cairo to discuss transitioning to the second phase of the Gaza ceasefire and increasing joint efforts coordinated with the United States . 

A source familiar with the discussions noted that the officials “agreed to continue strengthening coordination and cooperation with the Civil Military Coordination Center to eliminate all obstacles to ensure the continuity of the ceasefire and to prevent further violations.” This tripartite coordination mechanism has become essential for addressing the ongoing violations that threaten to derail the peace process . 

The United States has maintained its support for the Trump administration’s 20-point plan, which includes provisions for an international force to eventually replace Israeli troops in Gaza. A senior U.S. official revealed that Washington has drafted a resolution for the UN Security Council that would authorize this international force to “take all necessary measures to execute its mandate, including protecting civilians and ensuring Israeli military withdrawal” . 

Israeli Prime Minister Benjamin Netanyahu has conditioned acceptance of such a force, stating that the only military units that could enter Gaza as part of an international force would be those “Israel can accept” . This position reflects Israel’s ongoing security concerns about Hamas and PIJ rebuilding their military capabilities if the IDF withdraws completely without adequate security arrangements. 

7. Conclusion: A Fragile Peace

The recent operations in Rafah and the transfer of hostage remains represent both the fragile cooperation between adversaries and the persistent threats to the ceasefire agreement. While the diplomatic framework remains in place, the ongoing violence demonstrates how quickly localized incidents can escalate, potentially unravelling months of painstaking negotiation. 

The humanitarian situation continues to deteriorate, with the UN warning that “the systematic destruction of Gaza City is already underway” . The international community faces the dual challenge of maintaining the ceasefire while addressing a humanitarian catastrophe that has left most of Gaza’s population displaced, hungry, and without access to basic services. 

As winter sets in and conditions worsen for the displaced population, the need for sustainable solutions becomes increasingly urgent. The current ceasefire provides a window of opportunity not just for diplomatic arrangements between warring parties, but for addressing the deepening human suffering that threatens to leave lasting scars on generations of Palestinians and Israelis alike. 

The path forward remains uncertain, but what is clear is that without meaningful progress on both security concerns and humanitarian needs, the cycle of violence and brief respites that has characterized this conflict will likely continue, with ordinary civilians paying the heaviest price.