diff --git a/scripts/setup-genomes.sh b/scripts/setup-genomes.sh
index 4de8ed8..1add46a 100644
--- a/scripts/setup-genomes.sh
+++ b/scripts/setup-genomes.sh
@@ -2,7 +2,6 @@
 # =============================================================================
 # scripts/setup-genomes.sh
 # Iterates through the GENOMES registry to provision remote and local repos.
-# Handles git-crypt initialization and submodule linking.
 # =============================================================================
 
 set -euo pipefail
@@ -15,48 +14,44 @@ source "providers/${PROVIDER}.sh"
 step "Processing Genome Registry"
 
 for entry in "${GENOMES[@]}"; do
-    # Parse name and description from the array
     IFS='|' read -r GENOME_NAME GENOME_DESC <<< "$entry"
     export GENOME_NAME GENOME_DESC
 
     info "Processing: ${GENOME_NAME}..."
 
-    # 1. Remote Provisioning (Idempotent: skips if exists)
+    # 1. Remote Creation (Idempotent)
     provider_create_repo "${GENOME_NAME}" "${GENOME_DESC}" "true"
+    SSH_URL=$(provider_ssh_url "${GENOME_NAME}")
 
     GENOME_PATH="${WORK_DIR}/${MASTER_REPO}/${GENOME_NAME}"
 
     if [ ! -d "${GENOME_PATH}" ]; then
-        info "Creating local directory and initializing scaffold..."
-        mkdir -p "${GENOME_PATH}"
-        cd "${GENOME_PATH}"
-        git init
+        cd "${WORK_DIR}/${MASTER_REPO}"
+        info "Linking ${GENOME_NAME} as a submodule..."
 
-        # IMPORTANT: Initialize git-crypt BEFORE creating sensitive files
+        # FIX BUG 1: Adding the submodule clones the empty remote repository
+        git submodule add "${SSH_URL}" "${GENOME_NAME}"
+
+        cd "${GENOME_NAME}"
+
+        # IMPORTANT: Initialize git-crypt BEFORE creating any files
         gcrypt_init
 
-        # Create directory structure and apply templates
         scaffold_genome "."
         install_precommit_hook "."
 
-        # Initial commit and push to remote
+        # Initial genome push
         git add .
-        git commit -m "feat: initial scaffold for ${GENOME_NAME}"
-
-        SSH_URL=$(provider_ssh_url "${GENOME_NAME}")
-        git remote add origin "${SSH_URL}"
+        git commit -m "feat: initial scaffold and git-crypt init for ${GENOME_NAME}"
         git push -u origin main
 
-        # Export the AES key for the user to back up
+        # Key export and instructions (Fix Obs B)
         gcrypt_export_key "${GENOME_NAME}"
+        gcrypt_print_key_instructions "${GENOME_NAME}"
 
-        # 2. Link as submodule in the Master repository
+        # Return to master to consolidate the submodule addition
         cd "${WORK_DIR}/${MASTER_REPO}"
-        info "Linking ${GENOME_NAME} as a submodule..."
-        git submodule add "${SSH_URL}" "${GENOME_NAME}"
-        git add .gitmodules "${GENOME_NAME}"
-        git commit -m "feat: link submodule ${GENOME_NAME}"
-    else
-        warn "Genome directory '${GENOME_NAME}' already exists. Skipping local setup."
     fi
 done
+
+success "Genome provisioning completed."