diff --git a/crates/omnigraph-cli/src/main.rs b/crates/omnigraph-cli/src/main.rs
index 29f6f97..37e17f5 100644
--- a/crates/omnigraph-cli/src/main.rs
+++ b/crates/omnigraph-cli/src/main.rs
@@ -73,6 +73,13 @@ enum Command {
         schema: PathBuf,
         /// Graph URI (local path or s3://)
         uri: String,
+        /// Overwrite existing schema artifacts at the URI. Without
+        /// this flag, init refuses to touch a URI that already holds
+        /// `_schema.pg`, `_schema.ir.json`, or `__schema_state.json`
+        /// — closes the re-init footgun (MR-668 follow-up). With the
+        /// flag, the operator opts in to destructive semantics.
+        #[arg(long)]
+        force: bool,
     },
     /// Load data into a graph
     Load {
@@ -1746,10 +1753,15 @@ async fn main() -> Result<()> {
                 print_embed_human(&output);
             }
         }
-        Command::Init { schema, uri } => {
+        Command::Init { schema, uri, force } => {
             let schema_source = fs::read_to_string(&schema)?;
             ensure_local_graph_parent(&uri)?;
-            Omnigraph::init(&uri, &schema_source).await?;
+            Omnigraph::init_with_options(
+                &uri,
+                &schema_source,
+                omnigraph::db::InitOptions { force },
+            )
+            .await?;
             scaffold_config_if_missing(&uri)?;
             println!("initialized {}", uri);
         }
diff --git a/crates/omnigraph-server/src/lib.rs b/crates/omnigraph-server/src/lib.rs
index 42ee7a3..c20aee7 100644
--- a/crates/omnigraph-server/src/lib.rs
+++ b/crates/omnigraph-server/src/lib.rs
@@ -684,6 +684,12 @@ impl ApiError {
             // engine gate fires, the bearer is valid — any failure from
             // the engine is a policy outcome, not an auth one.
             OmniError::Policy(message) => Self::forbidden(message),
+            // `Omnigraph::init` against an existing graph URI in strict
+            // mode. Not currently HTTP-reachable (POST /graphs was
+            // pulled), but mapping is wired so the variant has a
+            // single canonical translation when a future runtime
+            // create endpoint lands.
+            err @ OmniError::AlreadyInitialized { .. } => Self::conflict(err.to_string()),
         }
     }
 }
diff --git a/crates/omnigraph/src/db/mod.rs b/crates/omnigraph/src/db/mod.rs
index 6bdd9ee..ce3d42a 100644
--- a/crates/omnigraph/src/db/mod.rs
+++ b/crates/omnigraph/src/db/mod.rs
@@ -11,7 +11,7 @@ pub use commit_graph::GraphCommit;
 pub use graph_coordinator::{GraphCoordinator, ReadTarget, ResolvedTarget, SnapshotId};
 pub use manifest::{Snapshot, SubTableEntry, SubTableUpdate};
 pub use omnigraph::{
-    CleanupPolicyOptions, MergeOutcome, Omnigraph, OpenMode, SchemaApplyOptions,
+    CleanupPolicyOptions, InitOptions, MergeOutcome, Omnigraph, OpenMode, SchemaApplyOptions,
     SchemaApplyResult, TableCleanupStats, TableOptimizeStats,
 };
 pub(crate) use omnigraph::ensure_public_branch_ref;
diff --git a/crates/omnigraph/src/db/omnigraph.rs b/crates/omnigraph/src/db/omnigraph.rs
index f3df8fb..c1d23e3 100644
--- a/crates/omnigraph/src/db/omnigraph.rs
+++ b/crates/omnigraph/src/db/omnigraph.rs
@@ -165,29 +165,92 @@ pub enum OpenMode {
     ReadOnly,
 }
 
+/// Options for [`Omnigraph::init_with_options`].
+///
+/// `force` controls the safety preflight that prevents an
+/// accidental re-init from overwriting an existing graph's schema
+/// metadata. Default behavior (`force: false`) fails fast with
+/// [`OmniError::AlreadyInitialized`] if any of `_schema.pg`,
+/// `_schema.ir.json`, or `__schema_state.json` already exists at
+/// the target URI. With `force: true` the preflight is skipped —
+/// existing schema files are overwritten in place. Force does NOT
+/// purge old Lance datasets or `__manifest/`; reclaiming those
+/// still requires deleting the graph directory by hand (or via a
+/// future `DELETE /graphs/{id}`).
+#[derive(Debug, Clone, Copy, Default)]
+pub struct InitOptions {
+    /// Skip the existing-graph preflight. Operators set this when
+    /// they actually mean to overwrite — e.g. `omnigraph init --force`.
+    pub force: bool,
+}
+
 impl Omnigraph {
     /// Create a new graph at `uri` from schema source.
     ///
-    /// Creates `_schema.pg`, per-type Lance datasets, and `__manifest`.
+    /// Strict mode: errors with [`OmniError::AlreadyInitialized`] if
+    /// `uri` already holds any of the three schema artifacts. To
+    /// overwrite an existing graph deliberately, call
+    /// [`Self::init_with_options`] with `InitOptions { force: true }`.
     pub async fn init(uri: &str, schema_source: &str) -> Result<Self> {
-        Self::init_with_storage(uri, schema_source, storage_for_uri(uri)?).await
+        Self::init_with_options(uri, schema_source, InitOptions::default()).await
+    }
+
+    /// Create a new graph at `uri`, with explicit init-time options.
+    ///
+    /// See [`InitOptions`] for the safety contract — by default this
+    /// behaves identically to [`Self::init`].
+    pub async fn init_with_options(
+        uri: &str,
+        schema_source: &str,
+        options: InitOptions,
+    ) -> Result<Self> {
+        Self::init_with_storage(uri, schema_source, storage_for_uri(uri)?, options).await
     }
 
     pub(crate) async fn init_with_storage(
         uri: &str,
         schema_source: &str,
         storage: Arc<dyn StorageAdapter>,
+        options: InitOptions,
     ) -> Result<Self> {
         let root = normalize_root_uri(uri)?;
+
+        // Preflight: refuse to clobber an existing graph unless the
+        // operator passed `force`. This runs BEFORE any parse or
+        // write so a misdirected `init` against an existing graph
+        // URI cannot reach a code path that overwrites or, on a
+        // later cleanup, deletes the schema files.
+        //
+        // Closes the "init is destructive against existing state"
+        // class: there is no longer a code path where strict-mode
+        // `init` can mutate a populated graph root.
+        if !options.force {
+            for candidate in [
+                schema_source_uri(&root),
+                schema_ir_uri(&root),
+                schema_state_uri(&root),
+            ] {
+                if storage.exists(&candidate).await? {
+                    return Err(OmniError::AlreadyInitialized {
+                        uri: root.clone(),
+                    });
+                }
+            }
+        }
+
         let schema_ir = read_schema_ir_from_source(schema_source)?;
         let mut catalog = build_catalog_from_ir(&schema_ir)?;
         fixup_blob_schemas(&mut catalog);
 
         // Run the I/O phase. On any error, best-effort-clean the schema
         // artifacts that may have been written to disk before returning
-        // the original error. The cleanup is best-effort: a failure to
-        // delete is logged via `tracing::warn` but does not mask the
-        // original init error.
+        // the original error. The cleanup is safe in strict mode because
+        // the preflight above guarantees the three schema URIs did NOT
+        // exist before this call, so any file there afterward is ours
+        // to delete. In `force` mode the operator opted in to overwrite
+        // semantics, so cleanup-on-failure of force re-inits may delete
+        // schema files that were present pre-call — that's part of the
+        // force contract.
         //
         // Coverage gap: Lance per-type datasets and `__manifest/`
         // directory created by `GraphCoordinator::init` are NOT cleaned
@@ -1852,7 +1915,7 @@ edge WorksAt: Person -> Company
         let uri = dir.path().to_str().unwrap();
         let adapter = Arc::new(RecordingStorageAdapter::default());
 
-        Omnigraph::init_with_storage(uri, TEST_SCHEMA, adapter.clone())
+        Omnigraph::init_with_storage(uri, TEST_SCHEMA, adapter.clone(), InitOptions::default())
             .await
             .unwrap();
         assert!(adapter.writes().contains(&join_uri(uri, "_schema.pg")));
diff --git a/crates/omnigraph/src/error.rs b/crates/omnigraph/src/error.rs
index 5d27fcb..11f4da0 100644
--- a/crates/omnigraph/src/error.rs
+++ b/crates/omnigraph/src/error.rs
@@ -92,6 +92,14 @@ pub enum OmniError {
     /// callers can match on this variant directly.
     #[error("policy: {0}")]
     Policy(String),
+    /// `Omnigraph::init` was called against a URI that already holds
+    /// schema artifacts from a previous init. Strict mode (the default)
+    /// fails fast with this error before touching disk so an existing
+    /// graph's metadata cannot be overwritten or destroyed. Operators
+    /// who actually want to overwrite pass `InitOptions { force: true }`
+    /// (CLI: `omnigraph init --force`).
+    #[error("graph already initialized at '{uri}'; pass --force to overwrite")]
+    AlreadyInitialized { uri: String },
 }
 
 impl OmniError {