diff --git a/internal/cmd/doctor.go b/internal/cmd/doctor.go
index a00c68fb..39654458 100644
--- a/internal/cmd/doctor.go
+++ b/internal/cmd/doctor.go
@@ -29,6 +29,10 @@ Cleanup checks (fixable):
   - orphan-processes         Detect orphaned Claude processes
   - wisp-gc                  Detect and clean abandoned wisps (>1h)
 
+Clone divergence checks:
+  - persistent-role-branches Detect crew/witness/refinery not on main
+  - clone-divergence         Detect clones significantly behind origin/main
+
 Patrol checks:
   - patrol-molecules-exist   Verify patrol molecules exist
   - patrol-hooks-wired       Verify daemon triggers patrols
@@ -75,6 +79,7 @@ func runDoctor(cmd *cobra.Command, args []string) error {
 	d.Register(doctor.NewWispGCCheck())
 	d.Register(doctor.NewBranchCheck())
 	d.Register(doctor.NewBeadsSyncOrphanCheck())
+	d.Register(doctor.NewCloneDivergenceCheck())
 	d.Register(doctor.NewIdentityCollisionCheck())
 	d.Register(doctor.NewLinkedPaneCheck())
 	d.Register(doctor.NewThemeCheck())
diff --git a/internal/doctor/branch_check.go b/internal/doctor/branch_check.go
index 3f11a6dd..71b86972 100644
--- a/internal/doctor/branch_check.go
+++ b/internal/doctor/branch_check.go
@@ -322,3 +322,226 @@ func (c *BeadsSyncOrphanCheck) findCrewDirs(townRoot string) []string {
 
 	return dirs
 }
+
+// CloneDivergenceCheck detects when git clones have drifted significantly apart.
+// This is an emergency condition - all clones should be tracking origin/main
+// and staying reasonably in sync. Divergence here is different from beads-sync
+// divergence, which is expected.
+type CloneDivergenceCheck struct {
+	BaseCheck
+}
+
+// NewCloneDivergenceCheck creates a new clone divergence check.
+func NewCloneDivergenceCheck() *CloneDivergenceCheck {
+	return &CloneDivergenceCheck{
+		BaseCheck: BaseCheck{
+			CheckName:        "clone-divergence",
+			CheckDescription: "Detect emergency divergence between git clones",
+		},
+	}
+}
+
+// cloneInfo holds information about a single clone.
+type cloneInfo struct {
+	path     string
+	branch   string
+	headSHA  string
+	behindBy int // commits behind origin/main
+}
+
+// Run checks for significant divergence between clones.
+func (c *CloneDivergenceCheck) Run(ctx *CheckContext) *CheckResult {
+	clones := c.findAllClones(ctx.TownRoot)
+	if len(clones) == 0 {
+		return &CheckResult{
+			Name:    c.Name(),
+			Status:  StatusOK,
+			Message: "No clones found",
+		}
+	}
+
+	// Gather info about each clone
+	var infos []cloneInfo
+	for _, path := range clones {
+		info, err := c.getCloneInfo(path)
+		if err != nil {
+			continue // Skip problematic clones
+		}
+		infos = append(infos, info)
+	}
+
+	if len(infos) == 0 {
+		return &CheckResult{
+			Name:    c.Name(),
+			Status:  StatusOK,
+			Message: "No valid git clones found",
+		}
+	}
+
+	// Check for clones significantly behind origin/main
+	var warnings []string
+	var errors []string
+
+	for _, info := range infos {
+		relPath := c.relativePath(ctx.TownRoot, info.path)
+
+		// Only check clones on main branch (others are caught by BranchCheck)
+		if info.branch != "main" && info.branch != "master" {
+			continue
+		}
+
+		if info.behindBy > 50 {
+			errors = append(errors, fmt.Sprintf("%s: %d commits behind origin/main (EMERGENCY)", relPath, info.behindBy))
+		} else if info.behindBy > 10 {
+			warnings = append(warnings, fmt.Sprintf("%s: %d commits behind origin/main", relPath, info.behindBy))
+		}
+	}
+
+	if len(errors) > 0 {
+		return &CheckResult{
+			Name:    c.Name(),
+			Status:  StatusError,
+			Message: fmt.Sprintf("%d clone(s) critically diverged", len(errors)),
+			Details: append(errors, warnings...),
+			FixHint: "Run 'git pull --rebase' in affected directories",
+		}
+	}
+
+	if len(warnings) > 0 {
+		return &CheckResult{
+			Name:    c.Name(),
+			Status:  StatusWarning,
+			Message: fmt.Sprintf("%d clone(s) behind origin/main", len(warnings)),
+			Details: warnings,
+			FixHint: "Run 'git pull --rebase' in affected directories",
+		}
+	}
+
+	return &CheckResult{
+		Name:    c.Name(),
+		Status:  StatusOK,
+		Message: fmt.Sprintf("All %d clones in sync with origin/main", len(infos)),
+	}
+}
+
+// findAllClones finds all git clones in the workspace.
+func (c *CloneDivergenceCheck) findAllClones(townRoot string) []string {
+	var clones []string
+
+	entries, err := os.ReadDir(townRoot)
+	if err != nil {
+		return clones
+	}
+
+	for _, entry := range entries {
+		if !entry.IsDir() || strings.HasPrefix(entry.Name(), ".") || entry.Name() == "mayor" || entry.Name() == "docs" {
+			continue
+		}
+
+		rigPath := filepath.Join(townRoot, entry.Name())
+
+		// Check standard clone locations
+		locations := []string{
+			"mayor/rig",
+			"witness/rig",
+			"refinery/rig",
+		}
+
+		for _, loc := range locations {
+			path := filepath.Join(rigPath, loc)
+			if c.isGitRepo(path) {
+				clones = append(clones, path)
+			}
+		}
+
+		// Add crew members
+		crewPath := filepath.Join(rigPath, "crew")
+		if crewEntries, err := os.ReadDir(crewPath); err == nil {
+			for _, crew := range crewEntries {
+				if crew.IsDir() && !strings.HasPrefix(crew.Name(), ".") {
+					path := filepath.Join(crewPath, crew.Name())
+					if c.isGitRepo(path) {
+						clones = append(clones, path)
+					}
+				}
+			}
+		}
+
+		// Add polecats
+		polecatsPath := filepath.Join(rigPath, "polecats")
+		if polecatEntries, err := os.ReadDir(polecatsPath); err == nil {
+			for _, polecat := range polecatEntries {
+				if polecat.IsDir() && !strings.HasPrefix(polecat.Name(), ".") {
+					path := filepath.Join(polecatsPath, polecat.Name())
+					if c.isGitRepo(path) {
+						clones = append(clones, path)
+					}
+				}
+			}
+		}
+	}
+
+	return clones
+}
+
+// isGitRepo checks if a directory is a git repository.
+func (c *CloneDivergenceCheck) isGitRepo(path string) bool {
+	gitDir := filepath.Join(path, ".git")
+	if _, err := os.Stat(gitDir); err == nil {
+		return true
+	}
+	return false
+}
+
+// getCloneInfo gathers information about a clone.
+func (c *CloneDivergenceCheck) getCloneInfo(path string) (cloneInfo, error) {
+	info := cloneInfo{path: path}
+
+	// Get current branch
+	cmd := exec.Command("git", "branch", "--show-current")
+	cmd.Dir = path
+	out, err := cmd.Output()
+	if err != nil {
+		return info, err
+	}
+	info.branch = strings.TrimSpace(string(out))
+
+	// Get HEAD SHA
+	cmd = exec.Command("git", "rev-parse", "HEAD")
+	cmd.Dir = path
+	out, err = cmd.Output()
+	if err != nil {
+		return info, err
+	}
+	info.headSHA = strings.TrimSpace(string(out))
+
+	// Fetch to make sure we have latest refs (silent, ignore errors)
+	cmd = exec.Command("git", "fetch", "--quiet")
+	cmd.Dir = path
+	_ = cmd.Run()
+
+	// Count commits behind origin/main
+	cmd = exec.Command("git", "rev-list", "--count", "HEAD..origin/main")
+	cmd.Dir = path
+	out, err = cmd.Output()
+	if err != nil {
+		// origin/main might not exist, treat as 0 behind
+		info.behindBy = 0
+		return info, nil
+	}
+
+	var behind int
+	_, _ = fmt.Sscanf(strings.TrimSpace(string(out)), "%d", &behind)
+	info.behindBy = behind
+
+	return info, nil
+}
+
+// relativePath returns path relative to base.
+func (c *CloneDivergenceCheck) relativePath(base, path string) string {
+	rel, err := filepath.Rel(base, path)
+	if err != nil {
+		return path
+	}
+	return rel
+}