diff --git a/Cargo.toml b/Cargo.toml
index 902ac92..beaa8f2 100644
--- a/Cargo.toml
+++ b/Cargo.toml
@@ -6,6 +6,9 @@ members = [
     "crates/neuron-api",
     "crates/neuron-protocol",
     "crates/axon-events",
+    "crates/neuron-runtime",
+    "crates/neuron-migrate",
+    "crates/neuron-cli",
 ]
 
 [workspace.dependencies]
diff --git a/crates/neuron-api/Cargo.toml b/crates/neuron-api/Cargo.toml
index 09605ae..2733731 100644
--- a/crates/neuron-api/Cargo.toml
+++ b/crates/neuron-api/Cargo.toml
@@ -11,6 +11,8 @@ path = "src/main.rs"
 neuron-domain = { path = "../neuron-domain" }
 neuron-store = { path = "../neuron-store" }
 neuron-protocol = { path = "../neuron-protocol" }
+neuron-runtime = { path = "../neuron-runtime" }
+chrono = { workspace = true }
 serde = { workspace = true }
 serde_json = { workspace = true }
 uuid = { workspace = true }
diff --git a/crates/neuron-api/src/routes/axon.rs b/crates/neuron-api/src/routes/axon.rs
index dbb8837..4514479 100644
--- a/crates/neuron-api/src/routes/axon.rs
+++ b/crates/neuron-api/src/routes/axon.rs
@@ -4,31 +4,53 @@ use axum::{
     Json,
 };
 use futures_util::Stream;
-use neuron_protocol::{AxonHandler, AxonMessage, AxonResponse};
+use neuron_protocol::{AxonMessage, AxonMethod, AxonResponse};
+use serde_json::Value;
 use std::sync::Arc;
 use std::time::Duration;
 
 use crate::state::AppState;
 
-/// POST /axon/message — receive an Axon protocol message and return a response.
+/// POST /axon/message — dispatch to NeuronRuntime.
 pub async fn post_message(
-    State(_state): State<Arc<AppState>>,
+    State(state): State<Arc<AppState>>,
     Json(msg): Json<AxonMessage>,
 ) -> Json<AxonResponse> {
-    let mut handler = AxonHandler::new();
+    match msg.method {
+        AxonMethod::ToolCall => {
+            let tool_name = msg
+                .params
+                .get("tool")
+                .and_then(|v| v.as_str())
+                .unwrap_or("")
+                .to_string();
+            let params = msg
+                .params
+                .get("params")
+                .cloned()
+                .unwrap_or(Value::Null);
 
-    // Register stub handlers for all known tool names.
-    for &tool in neuron_protocol::tools::ALL_TOOLS {
-        let name = tool.to_string();
-        handler.register(name, |params| {
-            serde_json::json!({
-                "status": "ok",
-                "params": params
-            })
-        });
+            if tool_name.is_empty() {
+                return Json(AxonResponse::err(msg.id, "missing 'tool' field in params"));
+            }
+
+            let result = state.runtime.dispatch(&tool_name, params).await;
+
+            // If the result contains an "error" field, surface it as an error response.
+            if let Some(err_msg) = result.get("error").and_then(|v| v.as_str()) {
+                Json(AxonResponse::err(msg.id, err_msg))
+            } else {
+                Json(AxonResponse::ok(msg.id, result))
+            }
+        }
+
+        AxonMethod::Ping => Json(AxonResponse::ok(
+            msg.id,
+            serde_json::json!({ "ts": chrono::Utc::now().to_rfc3339() }),
+        )),
+
+        _ => Json(AxonResponse::err(msg.id, "unsupported method")),
     }
-
-    Json(handler.dispatch(msg))
 }
 
 /// GET /axon/sse — Server-Sent Events stream for Axon events.
diff --git a/crates/neuron-api/src/state.rs b/crates/neuron-api/src/state.rs
index a517806..41527ab 100644
--- a/crates/neuron-api/src/state.rs
+++ b/crates/neuron-api/src/state.rs
@@ -1,4 +1,7 @@
 use std::path::Path;
+use std::sync::Arc;
+
+use neuron_runtime::NeuronRuntime;
 use neuron_store::{BacklogStore, ContextStore, IseStore, KnowledgeStore, MemoryStore, open_db};
 
 /// Shared application state — one store per domain.
@@ -12,17 +15,45 @@ pub struct AppState {
     pub context: ContextStore,
     pub ise: IseStore,
     pub api_key: String,
+    pub runtime: Arc<NeuronRuntime>,
 }
 
 impl AppState {
     pub fn new(db_path: &Path, api_key: String) -> Result<Self, neuron_domain::NeuronError> {
+        // Module directory defaults to "~/.neuron/lang" (or wherever .el files live).
+        // Falls back to a non-existent directory — runtime will have zero modules
+        // and fall back to native bindings for all tools.
+        let module_dir_raw =
+            std::env::var("NEURON_LANG_DIR").unwrap_or_else(|_| "~/.neuron/lang".to_string());
+        let module_dir = std::path::PathBuf::from(
+            module_dir_raw
+                .replace('~', &std::env::var("HOME").unwrap_or_else(|_| ".".to_string())),
+        );
+
+        // If the module directory doesn't exist, create an empty temp dir so
+        // load_directory doesn't error out.
+        let effective_dir = if module_dir.exists() {
+            module_dir
+        } else {
+            // Use a tmp dir — runtime will have zero modules (safe fallback).
+            std::env::temp_dir().join("neuron-lang-empty")
+        };
+        let _ = std::fs::create_dir_all(&effective_dir);
+
+        // Open the sled DB exactly once — Clone shares the same file lock.
+        let db = open_db(db_path)?;
+
+        let runtime = NeuronRuntime::from_dir(&effective_dir, db.clone())
+            .map_err(|e| neuron_domain::NeuronError::Storage(e.to_string()))?;
+
         Ok(Self {
-            memory: MemoryStore::new(open_db(db_path)?),
-            knowledge: KnowledgeStore::new(open_db(db_path)?),
-            backlog: BacklogStore::new(open_db(db_path)?),
-            context: ContextStore::new(open_db(db_path)?),
-            ise: IseStore::new(open_db(db_path)?),
+            memory: MemoryStore::new(db.clone()),
+            knowledge: KnowledgeStore::new(db.clone()),
+            backlog: BacklogStore::new(db.clone()),
+            context: ContextStore::new(db.clone()),
+            ise: IseStore::new(db),
             api_key,
+            runtime: Arc::new(runtime),
         })
     }
 }