diff --git a/server/src/chat/transport/matrix/assign.rs b/server/src/chat/transport/matrix/assign.rs
index f4008f51..8fc9b561 100644
--- a/server/src/chat/transport/matrix/assign.rs
+++ b/server/src/chat/transport/matrix/assign.rs
@@ -120,6 +120,10 @@ pub async fn handle_assign(
         return format!("Failed to assign model to **{story_name}**: {e}");
     }
 
+    // Mirror the assignment into the CRDT register so the in-memory pipeline
+    // state stays consistent with the front-matter.
+    crate::crdt_state::set_agent(&story_id, Some(&agent_name));
+
     // Check whether a coder is already running on this story.
     let running_coders: Vec<_> = agents
         .list_agents()
diff --git a/server/src/crdt_state/mod.rs b/server/src/crdt_state/mod.rs
index 270d89b8..cd43b833 100644
--- a/server/src/crdt_state/mod.rs
+++ b/server/src/crdt_state/mod.rs
@@ -53,7 +53,7 @@ pub use types::{
 };
 pub use write::{
     bump_retry_count, migrate_names_from_slugs, migrate_story_ids_to_numeric, name_from_story_id,
-    set_qa_mode, set_retry_count, write_item,
+    set_agent, set_qa_mode, set_retry_count, write_item,
 };
 
 #[cfg(test)]
diff --git a/server/src/crdt_state/write.rs b/server/src/crdt_state/write.rs
index b5e9f1cf..5bc05f26 100644
--- a/server/src/crdt_state/write.rs
+++ b/server/src/crdt_state/write.rs
@@ -186,6 +186,36 @@ pub fn migrate_names_from_slugs() {
     slog!("[crdt] Migrated names for {count} items from story ID slugs");
 }
 
+/// Set the `agent` field for a pipeline item by its story ID.
+///
+/// `Some(name)` writes the agent name into the CRDT register.
+/// `None` clears the register by writing an empty string — use this
+/// to unpin an agent without touching the surrounding item.
+///
+/// This is the typed setter counterpart to [`write_item`]'s `agent` parameter.
+/// Callers that only need to update the agent (e.g. the `update_story` MCP tool
+/// and the Matrix `!assign` command) should prefer this function over
+/// passing `agent` through the full [`write_item`] call, which requires all
+/// other fields to be known.
+///
+/// Returns `true` if the item was found and the write was performed.
+pub fn set_agent(story_id: &str, agent: Option<&str>) -> bool {
+    let Some(state_mutex) = get_crdt() else {
+        return false;
+    };
+    let Ok(mut state) = state_mutex.lock() else {
+        return false;
+    };
+    let Some(&idx) = state.index.get(story_id) else {
+        return false;
+    };
+    let value = agent.unwrap_or("").to_string();
+    apply_and_persist(&mut state, |s| {
+        s.crdt.doc.items[idx].agent.set(value.clone())
+    });
+    true
+}
+
 /// Set the typed `qa_mode` CRDT register for a pipeline item.
 ///
 /// Passing `Some(mode)` writes the mode string (e.g. `"server"`, `"agent"`, `"human"`)
@@ -685,6 +715,79 @@ mod tests {
         migrate_names_from_slugs();
     }
 
+    // ── set_agent tests ──────────────────────────────────────────────────────
+
+    #[test]
+    fn set_agent_some_writes_name() {
+        init_for_test();
+
+        write_item(
+            "871_story_set_agent_write",
+            "2_current",
+            Some("Set Agent Write"),
+            None,
+            None,
+            None,
+            None,
+            None,
+            None,
+            None,
+        );
+
+        let found = set_agent("871_story_set_agent_write", Some("coder-1"));
+        assert!(found, "set_agent should return true for an existing item");
+
+        let item = read_item("871_story_set_agent_write").expect("item must exist");
+        assert_eq!(
+            item.agent.as_deref(),
+            Some("coder-1"),
+            "agent should be written to CRDT register"
+        );
+    }
+
+    #[test]
+    fn set_agent_none_clears_register() {
+        init_for_test();
+
+        write_item(
+            "871_story_set_agent_clear",
+            "2_current",
+            Some("Set Agent Clear"),
+            Some("coder-2"),
+            None,
+            None,
+            None,
+            None,
+            None,
+            None,
+        );
+
+        // Confirm agent is set.
+        let before = read_item("871_story_set_agent_clear").expect("item must exist");
+        assert_eq!(before.agent.as_deref(), Some("coder-2"));
+
+        // Clear it.
+        let found = set_agent("871_story_set_agent_clear", None);
+        assert!(found, "set_agent should return true for an existing item");
+
+        let after = read_item("871_story_set_agent_clear").expect("item must exist");
+        assert!(
+            after.agent.as_deref().unwrap_or("").is_empty(),
+            "agent should be cleared (empty string) after set_agent(None)"
+        );
+    }
+
+    #[test]
+    fn set_agent_returns_false_for_unknown_story() {
+        init_for_test();
+
+        let found = set_agent("999_story_nonexistent", Some("coder-1"));
+        assert!(
+            !found,
+            "set_agent should return false when story is not in the CRDT"
+        );
+    }
+
     // ── set_qa_mode regression tests ─────────────────────────────────────────
 
     #[test]
diff --git a/server/src/http/mcp/story_tools/story/update.rs b/server/src/http/mcp/story_tools/story/update.rs
index 20f8abc0..a62692a0 100644
--- a/server/src/http/mcp/story_tools/story/update.rs
+++ b/server/src/http/mcp/story_tools/story/update.rs
@@ -44,6 +44,19 @@ pub(crate) fn tool_update_story(args: &Value, ctx: &AppContext) -> Result<String
         Some(&front_matter)
     };
 
+    // Capture the agent value before moving front_matter into the file writer,
+    // so we can mirror it into the CRDT register below.
+    let agent_for_crdt = args
+        .get("agent")
+        .and_then(|v| v.as_str())
+        .or_else(|| {
+            args.get("front_matter")
+                .and_then(|v| v.as_object())
+                .and_then(|o| o.get("agent"))
+                .and_then(|v| v.as_str())
+        })
+        .map(str::to_string);
+
     let root = ctx.state.get_project_root()?;
 
     // Only call update_story_in_file when there is something left to write.
@@ -51,6 +64,12 @@ pub(crate) fn tool_update_story(args: &Value, ctx: &AppContext) -> Result<String
         update_story_in_file(&root, story_id, user_story, description, front_matter_opt)?;
     }
 
+    // Mirror the agent assignment into the CRDT register so the in-memory
+    // pipeline state stays consistent with the front-matter.
+    if let Some(ref a) = agent_for_crdt {
+        crate::crdt_state::set_agent(story_id, Some(a));
+    }
+
     // Bug 503: warn if any depends_on in the (now updated) story points at an archived story.
     let stage = crate::pipeline_state::read_typed(story_id)
         .ok()