The latest instalment of the six-part film series Rebel Architecture opens with architect Eyal Weizman approaching one of the watchtowers along the separation wall that runs through the West Bank. An Israeli soldier shouts down, audible but invisible in the turret room: “Don’t come any closer!”

Weizman shouts back in response: “Why? Is this place only yours? It’s everybody’s place. Is that tube your home? It’s not even your home, and you’re sitting in that tube telling me what to do.”

Weizman has a reputation for being fearless. Fresh out of architecture school in London, the Haifa-born architect was commissioned along with colleague Rafi Seagal to showcase the best of Israeli architecture at the International Union of Architects Congress in Berlin, in 2002. He presented settlements. The Israel Association of United Architects withdrew their support, cancelled the exhibition and destroyed the catalogues. The move won him worldwide attention.

Since then, Weizman has also made a name for himself as the chief proponent of “forensic architecture”, by which he analyses the impacts of urban warfare for clues about the crimes that were perpetrated there. To Weizman, buildings are weapons. When he looks out across the landscape of the occupied Palestinian West Bank, as he does in the film The Architecture of Violence, to be aired on Al Jazeera today, he sees a battlefield. “The weapons and ammunitions are very simple elements: they are trees, they are terraces, they are houses. They are barriers.”

In the kitchen of his east London home, feeding me home-pickled cucumbers and endless cups of coffee, he says the most obvious and contentious aspect of what he calls the “architecture of occupation” is the system of Israeli settlements. Perched on West Bank hilltops, they are strategically positioned, according to Weizman, so that they look out over the Palestinian valleys and towns below, in order “to dominate”.

Each of the uniformly suburban-looking houses – all with the red roofs which he claims were once recommended by the military so that on flyovers the Israeli army knew not to target them – is “itself like an optical instrument,” he tells me. “When it is laid in rings around the hilltops, it is like a suburban-scale optical device that can survey the entire territory around it.” Around them, “settler only” roads operate as borders, connecting settlements with each other but splitting valleys in two, separating Palestinian farms, towns and cities from each other.

The second intifada, as well as fighting in Iraqi and Afghan cities in the early 2000s, showed him how war was migrating to the city. He used to work with the Palestinian ministry of planning, and was escorted by a bodyguard and forced to keep a keffiyeh on the bonnet of his car while driving around the West Bank. He now has his practice on “the other side of the wall”, in Beit Sahour, the West Bank town just outside of Bethlehem, where he co-runs the Decolonising Architecture Art Residency (Daar) with Palestinian architect Sandi Hilal and Italian architect Alessandro Petti, when he is not in London.

It was during the intifada that Weizman saw Israel quite deliberately and destructively reorganise cities to take away the upper hand from their defenders. The West Bank cities of Nablus and Jenin, for example, were laboratories for the development of urban warfare. When Israel tried to capture the heart of Jenin, “Palestine’s ground zero”, rather than exposing itself on the city’s existing roads the army used D9 bulldozers to carve out new avenues, flattening homes in the process.

Controversially, when Jenin was rebuilt by its residents after the army had left, they built a road now wide enough for tanks to be able to go through. They didn’t want the tanks to destroy their homes again. But they lost also their protection: the city’s density.

Another technique, used in Sejarah during the current conflict, is to drive armed carriers into buildings, often family homes, creating holes in the walls through which to deploy soldiers. The soldiers “immediately get saturated inside the buildings themselves … moving, because it’s so dense, between the one house and the other. Like worms moving inside apples.”

In this manner, architects can become “archaeologists of the present”, piecing together how things unfolded – which building was destroyed by artillery, which by tank fire, which by bulldozers. Weizman now leads the Forensic Architecture team at Goldsmiths, University of London – a unique project that provides “architectural evidence” for international prosecution teams, political organisations, NGOs and the UN. Their investigations include drone strikes, violence by state security forces on the Ixil Maya people in Guatemala and the use of white phosphorous in Gaza during Operation Cast Lead. They’ve also looked at Israel’s tactic of “knock on roof” warnings, which has been used extensively in the most recent conflict in Gaza.

“Cities are always about the links between buildings in the street, networks, infrastructure. When war happens in the city, people die in buildings, the majority in their own homes,” Weizman tells me. By carefully examining those buildings, you can find architectural evidence. If the Gaza conflict were ever to make it to the International Criminal Court, Weizman supposes he’d work with the prosecution: “We would show where there’s a violation of international law in the way in which buildings are attacked.” In this way, architects could play a role in reconstructing and therefore resisting violence.

Weizman believes this sort of architectural intelligence will be increasingly called on. He’s not alone: the Israel Defense Forces and the American and British militaries are establishing architectural academies for soldiers.

“As pathologists need to have medical intelligence to understand what happens to a body that was destroyed,” we also need to have “architectural intelligence to understand that violence,” Weizman says. And, just like a pathologist, he cuts a cross-section through his “specimens”.

“I’m looking at the sub-soil: archaeology, water, sewage, the valleys.” In the West Bank, for example, only small islands of space on the surface were given to the Palestinians to control as part of the Oslo accords. Israel kept sovereignty of other layers: the water aquifers, the air space. “Borders are not only on the surface,” he says. “You see it very clearly in Gaza through the tunnels and the rockets.”

For Weizman, though, it’s not all about architecture as a means of occupation, or as evidence of a crime. “It can open an arena of speculation on possible futures for Palestine that cannot yet be achieved; a kind of thinking laboratory.” While much of his work focuses on the dystopias created by architecture, he also imagines architectural solutions for a “shared future”. In this future, he imagines how settlements might be turned into Palestinian public institutions, and military bases into nature parks for migratory birds.

“Doesn’t he look ridiculous inside his pipe house?” Weizman says in the film after the encounter with the soldier. “Like, being the king of the hill, inside his tube.” Back in London, rocking in a chair by his kitchen window, he tries to sum up his feelings about the situation. “It’s a political commitment to all people – I won’t even say ‘both’, like there’s only Israelis and Palestinians. They are incredibly complex and multilayered societies, and I have so much love for this land and for the people that live there.”

The Architecture of Violence, directed by Ana de Sousa, airs on Al Jazeera English on 1 September. The film is part of the Rebel Architecture series. Hollow Land: Israel’s Architecture of Occupation by Eyal Weizman is published by Verso.

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• This article was amended on 4 August 2014 to remove an assertion that red roofs are mandatory in West Bank settlements