diff --git a/server/src/chat/commands/depends.rs b/server/src/chat/commands/depends.rs
index 705671c8..62cd6fd8 100644
--- a/server/src/chat/commands/depends.rs
+++ b/server/src/chat/commands/depends.rs
@@ -7,9 +7,7 @@
 //! Passing no dependency numbers clears the field entirely.
 
 use super::CommandContext;
-use crate::io::story_metadata::{
-    parse_front_matter, write_depends_on, write_depends_on_in_content,
-};
+use crate::io::story_metadata::parse_front_matter;
 
 /// Handle the `depends` command.
 ///
@@ -53,7 +51,7 @@ pub(super) fn handle_depends(ctx: &CommandContext) -> Option<String> {
     }
 
     // Find the story by numeric prefix: CRDT → content store → filesystem.
-    let (story_id, stage_dir, path, content) =
+    let (story_id, _stage_dir, _path, content) =
         match crate::chat::lookup::find_story_by_number(ctx.effective_root(), num_str) {
             Some(found) => found,
             None => {
@@ -69,49 +67,20 @@ pub(super) fn handle_depends(ctx: &CommandContext) -> Option<String> {
         .and_then(|m| m.name)
         .unwrap_or_else(|| story_id.clone());
 
-    // Prefer the CRDT content store; fall back to filesystem only when the
-    // story has not been loaded into the DB (e.g. very early startup or tests
-    // that haven't called write_item_with_content).
-    if let Some(existing) = crate::db::read_content(&story_id) {
-        let updated = write_depends_on_in_content(&existing, &deps);
-        crate::db::write_content(&story_id, &updated);
-        let stage = crate::pipeline_state::read_typed(&story_id)
-            .ok()
-            .flatten()
-            .map(|i| i.stage.dir_name().to_string())
-            .unwrap_or_else(|| stage_dir.clone());
-        crate::db::write_item_with_content(&story_id, &stage, &updated);
-        // Sync depends_on to the typed CRDT register.
-        crate::crdt_state::set_depends_on(&story_id, &deps);
-        if deps.is_empty() {
-            Some(format!(
-                "Cleared all dependencies for **{story_name}** ({story_id})."
-            ))
-        } else {
-            let nums: Vec<String> = deps.iter().map(|n| n.to_string()).collect();
-            Some(format!(
-                "Set depends_on: [{}] for **{story_name}** ({story_id}).",
-                nums.join(", ")
-            ))
-        }
+    // Write depends_on to the typed CRDT register — single source of truth.
+    // No YAML mutation: the CRDT register is the canonical location for deps.
+    crate::crdt_state::set_depends_on(&story_id, &deps);
+
+    if deps.is_empty() {
+        Some(format!(
+            "Cleared all dependencies for **{story_name}** ({story_id})."
+        ))
     } else {
-        match write_depends_on(&path, &deps) {
-            Ok(()) if deps.is_empty() => {
-                crate::crdt_state::set_depends_on(&story_id, &[]);
-                Some(format!(
-                    "Cleared all dependencies for **{story_name}** ({story_id})."
-                ))
-            }
-            Ok(()) => {
-                crate::crdt_state::set_depends_on(&story_id, &deps);
-                let nums: Vec<String> = deps.iter().map(|n| n.to_string()).collect();
-                Some(format!(
-                    "Set depends_on: [{}] for **{story_name}** ({story_id}).",
-                    nums.join(", ")
-                ))
-            }
-            Err(e) => Some(format!("Failed to update dependencies for {story_id}: {e}")),
-        }
+        let nums: Vec<String> = deps.iter().map(|n| n.to_string()).collect();
+        Some(format!(
+            "Set depends_on: [{}] for **{story_name}** ({story_id}).",
+            nums.join(", ")
+        ))
     }
 }
 
@@ -207,7 +176,7 @@ mod tests {
     }
 
     #[test]
-    fn depends_sets_deps_and_writes_to_content_store() {
+    fn depends_sets_deps_in_crdt_not_yaml() {
         let tmp = tempfile::TempDir::new().unwrap();
         write_story_file(
             tmp.path(),
@@ -220,33 +189,86 @@ mod tests {
             output.contains("477") && output.contains("478"),
             "response should mention dep numbers: {output}"
         );
-        let contents = crate::db::read_content("9910_story_foo")
-            .expect("content store should have updated story");
+        // CRDT register must hold the deps.
+        let view = crate::crdt_state::read_item("9910_story_foo").expect("CRDT should have story");
+        assert_eq!(
+            view.depends_on,
+            Some(vec![477, 478]),
+            "CRDT register should hold [477, 478]: {view:?}"
+        );
+        // Content store YAML must NOT be mutated with depends_on.
+        let contents =
+            crate::db::read_content("9910_story_foo").expect("content store should have story");
         assert!(
-            contents.contains("depends_on: [477, 478]"),
-            "content store should have depends_on set: {contents}"
+            !contents.contains("depends_on"),
+            "content store YAML must not contain depends_on after chat command: {contents}"
         );
     }
 
     #[test]
-    fn depends_clears_deps_when_no_deps_given() {
+    fn depends_clears_deps_in_crdt_not_yaml() {
         let tmp = tempfile::TempDir::new().unwrap();
         write_story_file(
             tmp.path(),
             "2_current",
             "9911_story_bar.md",
-            "---\nname: Bar\ndepends_on: [477]\n---\n",
+            "---\nname: Bar\n---\n",
         );
+        // Pre-seed CRDT with deps so we can verify clearing.
+        crate::crdt_state::set_depends_on("9911_story_bar", &[477]);
         let output = depends_cmd_with_root(tmp.path(), "9911").unwrap();
         assert!(
             output.contains("Cleared"),
             "should confirm clearing deps: {output}"
         );
-        let contents = crate::db::read_content("9911_story_bar")
-            .expect("content store should have updated story");
+        // CRDT register must be empty after clear.
+        let view = crate::crdt_state::read_item("9911_story_bar").expect("CRDT should have story");
+        assert_eq!(
+            view.depends_on, None,
+            "CRDT register should be empty after clearing: {view:?}"
+        );
+        // Content store YAML must not be mutated.
+        let contents =
+            crate::db::read_content("9911_story_bar").expect("content store should have story");
         assert!(
             !contents.contains("depends_on"),
-            "content store should have depends_on cleared: {contents}"
+            "content store YAML must not contain depends_on after clear: {contents}"
+        );
+    }
+
+    /// Regression (AC3, chat path): chat `depends` must write deps to CRDT only —
+    /// no `depends_on` in the YAML content store.
+    /// The MCP counterpart is `tool_update_story_depends_on_routes_to_crdt_not_yaml`
+    /// in `http/mcp/story_tools/story/update.rs`. Both assert `Some(vec![500, 501])`
+    /// proving identical CRDT state across transports.
+    #[test]
+    fn chat_depends_sets_crdt_no_yaml_regression() {
+        let tmp = tempfile::TempDir::new().unwrap();
+        write_story_file(
+            tmp.path(),
+            "1_backlog",
+            "8790_story_chat_dep.md",
+            "---\nname: Chat Dep\n---\n",
+        );
+
+        let out = depends_cmd_with_root(tmp.path(), "8790 500 501").unwrap();
+        assert!(
+            out.contains("500"),
+            "chat response should mention dep: {out}"
+        );
+
+        let view =
+            crate::crdt_state::read_item("8790_story_chat_dep").expect("CRDT must have chat story");
+        assert_eq!(
+            view.depends_on,
+            Some(vec![500, 501]),
+            "CRDT must hold [500, 501]: {view:?}"
+        );
+
+        let content = crate::db::read_content("8790_story_chat_dep").unwrap();
+        assert!(
+            !content.contains("depends_on"),
+            "chat must not write depends_on to YAML: {content}"
         );
     }
 
diff --git a/server/src/http/mcp/story_tools/story/update.rs b/server/src/http/mcp/story_tools/story/update.rs
index 07331510..d25081ba 100644
--- a/server/src/http/mcp/story_tools/story/update.rs
+++ b/server/src/http/mcp/story_tools/story/update.rs
@@ -41,8 +41,10 @@ pub(crate) fn tool_update_story(args: &Value, ctx: &AppContext) -> Result<String
         crate::crdt_state::set_qa_mode(story_id, mode);
     }
 
-    // Sync `depends_on` to the typed CRDT register when present in the update.
-    if let Some(deps_val) = front_matter.get("depends_on") {
+    // Route `depends_on` to the typed CRDT register and remove it from the
+    // front-matter map so it is NOT written back to the YAML content store.
+    // This matches the `qa` field pattern: CRDT is the single source of truth.
+    if let Some(deps_val) = front_matter.remove("depends_on") {
         if let Some(arr) = deps_val.as_array() {
             let dep_nums: Vec<u32> = arr
                 .iter()
@@ -148,7 +150,7 @@ mod tests {
         fs::create_dir_all(&current).unwrap();
         fs::write(current.join(format!("{story_id}.md")), content).unwrap();
         crate::db::ensure_content_store();
-        crate::db::write_content(story_id, content);
+        crate::db::write_item_with_content(story_id, "2_current", content);
     }
 
     #[test]
@@ -206,7 +208,7 @@ mod tests {
     }
 
     #[test]
-    fn tool_update_story_front_matter_json_array_written_as_yaml_sequence() {
+    fn tool_update_story_depends_on_routes_to_crdt_not_yaml() {
         let tmp = tempfile::tempdir().unwrap();
         setup_story_for_update(
             tmp.path(),
@@ -221,20 +223,19 @@ mod tests {
         );
         assert!(result.is_ok(), "Expected ok: {result:?}");
 
-        let content = crate::db::read_content("504_arr_test").unwrap();
-        // YAML inline sequences use spaces after commas
-        assert!(
-            content.contains("depends_on: [490, 491]"),
-            "array should be unquoted YAML: {content}"
-        );
-        assert!(
-            !content.contains("depends_on: \""),
-            "array must not be quoted: {content}"
+        // CRDT register must hold the deps.
+        let view = crate::crdt_state::read_item("504_arr_test").expect("CRDT must have the story");
+        assert_eq!(
+            view.depends_on,
+            Some(vec![490, 491]),
+            "CRDT register should hold [490, 491]: {view:?}"
         );
 
-        // The YAML must be parseable as a vec
-        let meta = crate::io::story_metadata::parse_front_matter(&content)
-            .expect("front matter should parse");
-        assert_eq!(meta.depends_on, Some(vec![490, 491]));
+        // Content store YAML must NOT contain depends_on — CRDT is sole source of truth.
+        let content = crate::db::read_content("504_arr_test").unwrap();
+        assert!(
+            !content.contains("depends_on"),
+            "depends_on must not be written to YAML content store: {content}"
+        );
     }
 }
diff --git a/server/src/io/story_metadata/fields.rs b/server/src/io/story_metadata/fields.rs
index d055582d..139f3752 100644
--- a/server/src/io/story_metadata/fields.rs
+++ b/server/src/io/story_metadata/fields.rs
@@ -94,25 +94,6 @@ pub fn write_review_hold(path: &Path) -> Result<(), String> {
     Ok(())
 }
 
-/// Write or update `depends_on:` field in the YAML front matter of a story file.
-///
-/// Serialises `deps` as an inline YAML sequence, e.g. `[477, 478]`.
-/// If `deps` is empty the field is removed.
-/// If no front matter is present, this is a no-op (returns Ok).
-pub fn write_depends_on(path: &Path, deps: &[u32]) -> Result<(), String> {
-    let contents =
-        fs::read_to_string(path).map_err(|e| format!("Failed to read story file: {e}"))?;
-    let updated = if deps.is_empty() {
-        remove_front_matter_field(&contents, "depends_on")
-    } else {
-        let nums: Vec<String> = deps.iter().map(|n| n.to_string()).collect();
-        let yaml_value = format!("[{}]", nums.join(", "));
-        set_front_matter_field(&contents, "depends_on", &yaml_value)
-    };
-    fs::write(path, &updated).map_err(|e| format!("Failed to write story file: {e}"))?;
-    Ok(())
-}
-
 /// Remove a key from the YAML front matter of a markdown string (pure function).
 ///
 /// Returns the updated content.  If no front matter or key is not found,
@@ -152,20 +133,6 @@ pub fn write_mergemaster_attempted_in_content(contents: &str) -> String {
     set_front_matter_field(contents, "mergemaster_attempted", "true")
 }
 
-/// Write or update `depends_on` in story content (pure function).
-///
-/// Serialises `deps` as an inline YAML sequence, e.g. `[477, 478]`.
-/// If `deps` is empty the field is removed.
-pub fn write_depends_on_in_content(contents: &str, deps: &[u32]) -> String {
-    if deps.is_empty() {
-        remove_front_matter_field(contents, "depends_on")
-    } else {
-        let nums: Vec<String> = deps.iter().map(|n| n.to_string()).collect();
-        let yaml_value = format!("[{}]", nums.join(", "));
-        set_front_matter_field(contents, "depends_on", &yaml_value)
-    }
-}
-
 #[cfg(test)]
 mod tests {
     use super::*;
@@ -242,24 +209,4 @@ mod tests {
         assert!(contents.contains("review_hold: true"));
         assert!(contents.contains("name: My Spike"));
     }
-
-    #[test]
-    fn write_depends_on_sets_field() {
-        let tmp = tempfile::tempdir().unwrap();
-        let path = tmp.path().join("story.md");
-        std::fs::write(&path, "---\nname: Test\n---\n# Story\n").unwrap();
-        write_depends_on(&path, &[477, 478]).unwrap();
-        let contents = std::fs::read_to_string(&path).unwrap();
-        assert!(contents.contains("depends_on: [477, 478]"), "{contents}");
-    }
-
-    #[test]
-    fn write_depends_on_removes_field_when_empty() {
-        let tmp = tempfile::tempdir().unwrap();
-        let path = tmp.path().join("story.md");
-        std::fs::write(&path, "---\nname: Test\ndepends_on: [477]\n---\n# Story\n").unwrap();
-        write_depends_on(&path, &[]).unwrap();
-        let contents = std::fs::read_to_string(&path).unwrap();
-        assert!(!contents.contains("depends_on"), "{contents}");
-    }
 }
diff --git a/server/src/io/story_metadata/mod.rs b/server/src/io/story_metadata/mod.rs
index 913a21d9..e07e0cab 100644
--- a/server/src/io/story_metadata/mod.rs
+++ b/server/src/io/story_metadata/mod.rs
@@ -14,9 +14,8 @@ mod types;
 pub use deps::{check_archived_deps, check_archived_deps_from_list, check_unmet_deps};
 pub use fields::{
     clear_front_matter_field, clear_front_matter_field_in_content, set_front_matter_field,
-    write_depends_on, write_depends_on_in_content, write_merge_failure_in_content,
-    write_mergemaster_attempted_in_content, write_rejection_notes_to_content, write_review_hold,
-    write_review_hold_in_content,
+    write_merge_failure_in_content, write_mergemaster_attempted_in_content,
+    write_rejection_notes_to_content, write_review_hold, write_review_hold_in_content,
 };
 pub use parser::{
     is_story_frozen_in_store, parse_front_matter, parse_unchecked_todos, resolve_qa_mode,