The Israeli perspective of the historic events currently under way in Egypt is quite different from those commonly found in western countries. The US and Europe are more likely to support the removal of a government that denies its citizens basic freedoms, while Israel's main concern is that the unrest in Egypt will have serious regional security implications. If Hosni Mubarak's regime collapses it could endanger the peace agreements Israel has with Jordan and Egypt, Israel's main strategic assets after its alliance with Washington. In the longer run, the new reality on its southern border may also require structural military changes and place an extra burden on the Israeli economy.

Israel's political leadership and security branches have been struggling to decode the US's Middle East policies. The surprise of Obama's speech in Cairo in 2009 has been replaced with amazement at just how quickly the US has abandoned its old ally. Like Jimmy Carter when the Iranian shah's regime collapsed in 1979, Obama is wavering between supporting a dedicated partner and the basic American inclination to back a popular freedom struggle. Like Carter, a Democrat, Obama chose the second option. Jerusalem has reservations about the American tendency to see events in Cairo as an Arabic version of the Boston tea party. In the Middle East people generally prefer bitter coffee.

Israel suspects that behind ordinary citizens protesting about the economic situation and election fraud stands a new Islamist order. The Muslim Brotherhood does not yet pull the strings, but it remains the only organised force within the Egyptian opposition. Israel believes that, if Mubarak falls, it will be first to recover and exploit the confusion and seize power.

Although the Brotherhood has threatened to pull out of talks, Israel is still worried that it might come out victorious. Seared in Israeli memory is a fresh precedent: in January 2006 parliamentary elections were held in the Palestinian territories, under pressure from President George W Bush. Hamas's victory encouraged its takeover of the Gaza Strip in June 2007. Today a radical Islamist regime is in control of Gaza, severely depressing its residents, much more repressive than the Mubarak regime – and of course very hostile to Israel.

If Mubarak is overthrown there will be serious consequences for Israel and its quiet co-operation with Egypt. It may also lead to a thaw between Egypt and the Hamas government in Gaza. It could damage the status of the international peacekeeping force in Sinai and lead to a refusal by Egypt to allow movement of Israeli military submarines and ships in the Suez Canal, employed in the last two years as a deterrent against Iran and to combat weapons-smuggling from the Red Sea to the Gaza Strip. In the long run, if a radical government gains power, there is likely to be a real freeze in the already cold peace with Israel.

For the army, this will require reorganisation. It is more than 20 years since it had to prepare to deal with a real threat from Egypt. The army is trained for clashes with Hezbollah and Hamas, at the most in combination with Syria. No one has seriously planned for a scenario in which, for example, Egypt identifies with Hamas in the event of an Israeli attack in Gaza.

The Israeli-Egyptian peace agreement, signed in 1979, enabled a gradual cutback in the deployment of forces, a reduction in the age of those exempt from reserve duty, and a sweeping diversion of resources toward social and economic goals, assisting the economic recovery in the mid-80s. This happened after the "lost decade" (1974-1984) in which Israel has invested huge sums to its army, following the trauma of the 1973 Yom Kippur War. It is still too soon to reach conclusions, but it seems that if the Mubarak regime collapses, the pendulum will swing back, and Israel will have to gradually prepare its army for worst-case scenarios. The 1973 intelligence failure was again mentioned this week, after both military intelligence the Mossad did not foresee the intensity of popular unrest in Egypt. In all fairness, neither did anybody else.

After that first turbulent weekend in Cairo, Benjamin Netanyahu, Israel's prime minister, asked his ministers not to speak on the subject due to its sensitivity. But he could not restrain himself at a press conference with German Chancellor Angela Merkel in Jerusalem, and warned against takeover of Egypt by a radical Islamist regime. The last thing Mubarak needed was a hug from Netanyahu – yet he got it. Anyone watching the broadcasts from Egypt could hear the protesters repeating words of hostility towards Israel in Independence Square. When Mubarak announced the appointment of the veteran intelligence minister Omar Suleiman as his deputy, al-Jazeera rushed to the archives to broadcast pictures of Suleiman with senior Israeli officials. The subtext was clear: the likely heir is an Israeli agent.

In recent years, Israeli spokesmen described the developments in the Middle East as a struggle between the moderates – primarily Egypt and Saudi Arabia – and Iran and its partners in radicalism. Events in Cairo indicate the moderate Sunni states are in retreat. Within Israel, the Egyptian revolution will be interpreted as an ideological victory for those warning against territorial concessions, even as part of a comprehensive peace agreement. For most of the public in Israel, the withdrawal of the Israel Defence Forces from South Lebanon (in 2000) and Gaza (in 2005) led to rocket fire from the territories that were evacuated. Now, as Cairo plunges into an uncertain transition, a question mark hangs even over the fate of the old peace agreement with Egypt. The conclusion of the right is clear – and has already been expressed in recent days: as long as its neighbours are undemocratic and under constant threat of an Islamist coup, Israel must not take unnecessary risks.

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