diff --git a/internal/cmd/doctor.go b/internal/cmd/doctor.go
index 30cc7542..b95f9aee 100644
--- a/internal/cmd/doctor.go
+++ b/internal/cmd/doctor.go
@@ -23,6 +23,13 @@ var doctorCmd = &cobra.Command{
 Doctor checks for common configuration issues, missing files,
 and other problems that could affect workspace operation.
 
+Patrol checks:
+  - patrol-molecules-exist   Verify patrol molecules exist
+  - patrol-hooks-wired       Verify daemon triggers patrols
+  - patrol-not-stuck         Detect stale wisps (>1h)
+  - patrol-plugins-accessible Verify plugin directories
+  - patrol-roles-have-prompts Verify role prompts exist
+
 Use --fix to attempt automatic fixes for issues that support it.
 Use --rig to check a specific rig instead of the entire workspace.`,
 	RunE: runDoctor,
@@ -71,6 +78,13 @@ func runDoctor(cmd *cobra.Command, args []string) error {
 	d.Register(doctor.NewWispSizeCheck())
 	d.Register(doctor.NewWispStaleCheck())
 
+	// Patrol system checks
+	d.Register(doctor.NewPatrolMoleculesExistCheck())
+	d.Register(doctor.NewPatrolHooksWiredCheck())
+	d.Register(doctor.NewPatrolNotStuckCheck())
+	d.Register(doctor.NewPatrolPluginsAccessibleCheck())
+	d.Register(doctor.NewPatrolRolesHavePromptsCheck())
+
 	// Config architecture checks
 	d.Register(doctor.NewSettingsCheck())
 	d.Register(doctor.NewRuntimeGitignoreCheck())
diff --git a/internal/cmd/rig.go b/internal/cmd/rig.go
index d9860926..06a875dd 100644
--- a/internal/cmd/rig.go
+++ b/internal/cmd/rig.go
@@ -45,12 +45,18 @@ This creates a rig container with:
   - config.json           Rig configuration
   - .beads/               Rig-level issue tracking (initialized)
   - .beads-wisp/          Local wisp/molecule tracking (gitignored)
+  - plugins/              Rig-level plugin directory
   - refinery/rig/         Canonical main clone
   - mayor/rig/            Mayor's working clone
   - crew/main/            Default human workspace
   - witness/              Witness agent directory
   - polecats/             Worker directory (empty)
 
+The command also:
+  - Seeds patrol molecules (Deacon, Witness, Refinery)
+  - Creates ~/gt/plugins/ (town-level) if it doesn't exist
+  - Creates <rig>/plugins/ (rig-level)
+
 Example:
   gt rig add gastown https://github.com/steveyegge/gastown
   gt rig add my-project git@github.com:user/repo.git --prefix mp`,
@@ -201,6 +207,7 @@ func runRigAdd(cmd *cobra.Command, args []string) error {
 	fmt.Printf("  ├── config.json\n")
 	fmt.Printf("  ├── .beads/           (prefix: %s)\n", newRig.Config.Prefix)
 	fmt.Printf("  ├── .beads-wisp/      (local wisp/molecule tracking)\n")
+	fmt.Printf("  ├── plugins/          (rig-level plugins)\n")
 	fmt.Printf("  ├── refinery/rig/     (canonical main)\n")
 	fmt.Printf("  ├── mayor/rig/        (mayor's clone)\n")
 	fmt.Printf("  ├── crew/%s/        (your workspace)\n", rigAddCrew)
diff --git a/internal/doctor/patrol_check.go b/internal/doctor/patrol_check.go
new file mode 100644
index 00000000..dcdf19f6
--- /dev/null
+++ b/internal/doctor/patrol_check.go
@@ -0,0 +1,459 @@
+package doctor
+
+import (
+	"bufio"
+	"encoding/json"
+	"fmt"
+	"os"
+	"os/exec"
+	"path/filepath"
+	"strings"
+	"time"
+)
+
+// PatrolMoleculesExistCheck verifies that patrol molecules exist for each rig.
+type PatrolMoleculesExistCheck struct {
+	FixableCheck
+	missingMols map[string][]string // rig -> missing molecule titles
+}
+
+// NewPatrolMoleculesExistCheck creates a new patrol molecules exist check.
+func NewPatrolMoleculesExistCheck() *PatrolMoleculesExistCheck {
+	return &PatrolMoleculesExistCheck{
+		FixableCheck: FixableCheck{
+			BaseCheck: BaseCheck{
+				CheckName:        "patrol-molecules-exist",
+				CheckDescription: "Check if patrol molecules exist for each rig",
+			},
+		},
+	}
+}
+
+// patrolMolecules are the required patrol molecule titles.
+var patrolMolecules = []string{
+	"Deacon Patrol",
+	"Witness Patrol",
+	"Refinery Patrol",
+}
+
+// Run checks if patrol molecules exist.
+func (c *PatrolMoleculesExistCheck) Run(ctx *CheckContext) *CheckResult {
+	c.missingMols = make(map[string][]string)
+
+	rigs, err := discoverRigs(ctx.TownRoot)
+	if err != nil {
+		return &CheckResult{
+			Name:    c.Name(),
+			Status:  StatusError,
+			Message: "Failed to discover rigs",
+			Details: []string{err.Error()},
+		}
+	}
+
+	if len(rigs) == 0 {
+		return &CheckResult{
+			Name:    c.Name(),
+			Status:  StatusOK,
+			Message: "No rigs configured",
+		}
+	}
+
+	var details []string
+	for _, rigName := range rigs {
+		rigPath := filepath.Join(ctx.TownRoot, rigName)
+		missing := c.checkPatrolMolecules(rigPath)
+		if len(missing) > 0 {
+			c.missingMols[rigName] = missing
+			details = append(details, fmt.Sprintf("%s: missing %v", rigName, missing))
+		}
+	}
+
+	if len(details) > 0 {
+		return &CheckResult{
+			Name:    c.Name(),
+			Status:  StatusWarning,
+			Message: fmt.Sprintf("%d rig(s) missing patrol molecules", len(c.missingMols)),
+			Details: details,
+			FixHint: "Run 'gt doctor --fix' to create missing patrol molecules",
+		}
+	}
+
+	return &CheckResult{
+		Name:    c.Name(),
+		Status:  StatusOK,
+		Message: fmt.Sprintf("All %d rig(s) have patrol molecules", len(rigs)),
+	}
+}
+
+// checkPatrolMolecules returns missing patrol molecule titles for a rig.
+func (c *PatrolMoleculesExistCheck) checkPatrolMolecules(rigPath string) []string {
+	// List molecules using bd
+	cmd := exec.Command("bd", "list", "--type=molecule")
+	cmd.Dir = rigPath
+	output, err := cmd.Output()
+	if err != nil {
+		return patrolMolecules // Can't check, assume all missing
+	}
+
+	outputStr := string(output)
+	var missing []string
+	for _, mol := range patrolMolecules {
+		if !strings.Contains(outputStr, mol) {
+			missing = append(missing, mol)
+		}
+	}
+	return missing
+}
+
+// Fix creates missing patrol molecules.
+func (c *PatrolMoleculesExistCheck) Fix(ctx *CheckContext) error {
+	for rigName, missing := range c.missingMols {
+		rigPath := filepath.Join(ctx.TownRoot, rigName)
+		for _, mol := range missing {
+			desc := getPatrolMoleculeDesc(mol)
+			cmd := exec.Command("bd", "create",
+				"--type=molecule",
+				"--title="+mol,
+				"--description="+desc,
+				"--priority=2",
+			)
+			cmd.Dir = rigPath
+			if err := cmd.Run(); err != nil {
+				return fmt.Errorf("creating %s in %s: %w", mol, rigName, err)
+			}
+		}
+	}
+	return nil
+}
+
+func getPatrolMoleculeDesc(title string) string {
+	switch title {
+	case "Deacon Patrol":
+		return "Mayor's daemon patrol loop for handling callbacks, health checks, and cleanup."
+	case "Witness Patrol":
+		return "Per-rig worker monitor patrol loop with progressive nudging."
+	case "Refinery Patrol":
+		return "Merge queue processor patrol loop with verification gates."
+	default:
+		return "Patrol molecule"
+	}
+}
+
+// PatrolHooksWiredCheck verifies that hooks trigger patrol execution.
+type PatrolHooksWiredCheck struct {
+	BaseCheck
+}
+
+// NewPatrolHooksWiredCheck creates a new patrol hooks wired check.
+func NewPatrolHooksWiredCheck() *PatrolHooksWiredCheck {
+	return &PatrolHooksWiredCheck{
+		BaseCheck: BaseCheck{
+			CheckName:        "patrol-hooks-wired",
+			CheckDescription: "Check if hooks trigger patrol execution",
+		},
+	}
+}
+
+// Run checks if patrol hooks are wired.
+func (c *PatrolHooksWiredCheck) Run(ctx *CheckContext) *CheckResult {
+	// Check for daemon config which manages patrols
+	daemonConfigPath := filepath.Join(ctx.TownRoot, "mayor", "daemon.json")
+	if _, err := os.Stat(daemonConfigPath); os.IsNotExist(err) {
+		return &CheckResult{
+			Name:    c.Name(),
+			Status:  StatusWarning,
+			Message: "Daemon config not found",
+			FixHint: "Run 'gt daemon init' to configure daemon",
+		}
+	}
+
+	// Check daemon config for patrol configuration
+	data, err := os.ReadFile(daemonConfigPath)
+	if err != nil {
+		return &CheckResult{
+			Name:    c.Name(),
+			Status:  StatusError,
+			Message: "Failed to read daemon config",
+			Details: []string{err.Error()},
+		}
+	}
+
+	var config map[string]interface{}
+	if err := json.Unmarshal(data, &config); err != nil {
+		return &CheckResult{
+			Name:    c.Name(),
+			Status:  StatusWarning,
+			Message: "Invalid daemon config format",
+			Details: []string{err.Error()},
+		}
+	}
+
+	// Check for patrol entries
+	if patrols, ok := config["patrols"]; ok {
+		if patrolMap, ok := patrols.(map[string]interface{}); ok && len(patrolMap) > 0 {
+			return &CheckResult{
+				Name:    c.Name(),
+				Status:  StatusOK,
+				Message: fmt.Sprintf("Daemon configured with %d patrol(s)", len(patrolMap)),
+			}
+		}
+	}
+
+	// Check if heartbeat is enabled (triggers deacon patrol)
+	if heartbeat, ok := config["heartbeat"]; ok {
+		if hb, ok := heartbeat.(map[string]interface{}); ok {
+			if enabled, ok := hb["enabled"].(bool); ok && enabled {
+				return &CheckResult{
+					Name:    c.Name(),
+					Status:  StatusOK,
+					Message: "Daemon heartbeat enabled (triggers patrols)",
+				}
+			}
+		}
+	}
+
+	return &CheckResult{
+		Name:    c.Name(),
+		Status:  StatusWarning,
+		Message: "Patrol hooks not configured in daemon",
+		FixHint: "Configure patrols in mayor/daemon.json or run 'gt daemon init'",
+	}
+}
+
+// PatrolNotStuckCheck detects wisps that have been in_progress too long.
+type PatrolNotStuckCheck struct {
+	BaseCheck
+	stuckThreshold time.Duration
+}
+
+// NewPatrolNotStuckCheck creates a new patrol not stuck check.
+func NewPatrolNotStuckCheck() *PatrolNotStuckCheck {
+	return &PatrolNotStuckCheck{
+		BaseCheck: BaseCheck{
+			CheckName:        "patrol-not-stuck",
+			CheckDescription: "Check for stuck patrol wisps (>1h in_progress)",
+		},
+		stuckThreshold: 1 * time.Hour,
+	}
+}
+
+// Run checks for stuck patrol wisps.
+func (c *PatrolNotStuckCheck) Run(ctx *CheckContext) *CheckResult {
+	rigs, err := discoverRigs(ctx.TownRoot)
+	if err != nil {
+		return &CheckResult{
+			Name:    c.Name(),
+			Status:  StatusError,
+			Message: "Failed to discover rigs",
+			Details: []string{err.Error()},
+		}
+	}
+
+	if len(rigs) == 0 {
+		return &CheckResult{
+			Name:    c.Name(),
+			Status:  StatusOK,
+			Message: "No rigs configured",
+		}
+	}
+
+	var stuckWisps []string
+	for _, rigName := range rigs {
+		wispPath := filepath.Join(ctx.TownRoot, rigName, ".beads-wisp", "issues.jsonl")
+		stuck := c.checkStuckWisps(wispPath, rigName)
+		stuckWisps = append(stuckWisps, stuck...)
+	}
+
+	if len(stuckWisps) > 0 {
+		return &CheckResult{
+			Name:    c.Name(),
+			Status:  StatusWarning,
+			Message: fmt.Sprintf("%d stuck patrol wisp(s) found (>1h)", len(stuckWisps)),
+			Details: stuckWisps,
+			FixHint: "Manual review required - wisps may need to be burned or sessions restarted",
+		}
+	}
+
+	return &CheckResult{
+		Name:    c.Name(),
+		Status:  StatusOK,
+		Message: "No stuck patrol wisps found",
+	}
+}
+
+// checkStuckWisps returns descriptions of stuck wisps in a rig.
+func (c *PatrolNotStuckCheck) checkStuckWisps(issuesPath string, rigName string) []string {
+	file, err := os.Open(issuesPath)
+	if err != nil {
+		return nil // No issues file
+	}
+	defer file.Close()
+
+	var stuck []string
+	cutoff := time.Now().Add(-c.stuckThreshold)
+
+	scanner := bufio.NewScanner(file)
+	for scanner.Scan() {
+		line := scanner.Text()
+		if line == "" {
+			continue
+		}
+
+		var issue struct {
+			ID        string    `json:"id"`
+			Title     string    `json:"title"`
+			Status    string    `json:"status"`
+			UpdatedAt time.Time `json:"updated_at"`
+		}
+		if err := json.Unmarshal([]byte(line), &issue); err != nil {
+			continue
+		}
+
+		// Check for in_progress issues older than threshold
+		if issue.Status == "in_progress" && !issue.UpdatedAt.IsZero() && issue.UpdatedAt.Before(cutoff) {
+			stuck = append(stuck, fmt.Sprintf("%s: %s (%s) - stale since %s",
+				rigName, issue.ID, issue.Title, issue.UpdatedAt.Format("2006-01-02 15:04")))
+		}
+	}
+
+	return stuck
+}
+
+// PatrolPluginsAccessibleCheck verifies plugin directories exist and are readable.
+type PatrolPluginsAccessibleCheck struct {
+	FixableCheck
+	missingDirs []string
+}
+
+// NewPatrolPluginsAccessibleCheck creates a new patrol plugins accessible check.
+func NewPatrolPluginsAccessibleCheck() *PatrolPluginsAccessibleCheck {
+	return &PatrolPluginsAccessibleCheck{
+		FixableCheck: FixableCheck{
+			BaseCheck: BaseCheck{
+				CheckName:        "patrol-plugins-accessible",
+				CheckDescription: "Check if plugin directories exist and are readable",
+			},
+		},
+	}
+}
+
+// Run checks if plugin directories are accessible.
+func (c *PatrolPluginsAccessibleCheck) Run(ctx *CheckContext) *CheckResult {
+	c.missingDirs = nil
+
+	// Check town-level plugins directory
+	townPluginsDir := filepath.Join(ctx.TownRoot, "plugins")
+	if _, err := os.Stat(townPluginsDir); os.IsNotExist(err) {
+		c.missingDirs = append(c.missingDirs, townPluginsDir)
+	}
+
+	// Check rig-level plugins directories
+	rigs, err := discoverRigs(ctx.TownRoot)
+	if err == nil {
+		for _, rigName := range rigs {
+			rigPluginsDir := filepath.Join(ctx.TownRoot, rigName, "plugins")
+			if _, err := os.Stat(rigPluginsDir); os.IsNotExist(err) {
+				c.missingDirs = append(c.missingDirs, rigPluginsDir)
+			}
+		}
+	}
+
+	if len(c.missingDirs) > 0 {
+		return &CheckResult{
+			Name:    c.Name(),
+			Status:  StatusWarning,
+			Message: fmt.Sprintf("%d plugin directory(ies) missing", len(c.missingDirs)),
+			Details: c.missingDirs,
+			FixHint: "Run 'gt doctor --fix' to create missing directories",
+		}
+	}
+
+	return &CheckResult{
+		Name:    c.Name(),
+		Status:  StatusOK,
+		Message: "All plugin directories accessible",
+	}
+}
+
+// Fix creates missing plugin directories.
+func (c *PatrolPluginsAccessibleCheck) Fix(ctx *CheckContext) error {
+	for _, dir := range c.missingDirs {
+		if err := os.MkdirAll(dir, 0755); err != nil {
+			return fmt.Errorf("creating %s: %w", dir, err)
+		}
+	}
+	return nil
+}
+
+// PatrolRolesHavePromptsCheck verifies that prompts/roles/*.md exist for each role.
+type PatrolRolesHavePromptsCheck struct {
+	BaseCheck
+}
+
+// NewPatrolRolesHavePromptsCheck creates a new patrol roles have prompts check.
+func NewPatrolRolesHavePromptsCheck() *PatrolRolesHavePromptsCheck {
+	return &PatrolRolesHavePromptsCheck{
+		BaseCheck: BaseCheck{
+			CheckName:        "patrol-roles-have-prompts",
+			CheckDescription: "Check if prompts/roles/*.md exist for each patrol role",
+		},
+	}
+}
+
+// requiredRolePrompts are the required role prompt files.
+var requiredRolePrompts = []string{
+	"deacon.md",
+	"witness.md",
+	"refinery.md",
+}
+
+// Run checks if role prompts exist.
+func (c *PatrolRolesHavePromptsCheck) Run(ctx *CheckContext) *CheckResult {
+	rigs, err := discoverRigs(ctx.TownRoot)
+	if err != nil {
+		return &CheckResult{
+			Name:    c.Name(),
+			Status:  StatusError,
+			Message: "Failed to discover rigs",
+			Details: []string{err.Error()},
+		}
+	}
+
+	if len(rigs) == 0 {
+		return &CheckResult{
+			Name:    c.Name(),
+			Status:  StatusOK,
+			Message: "No rigs configured",
+		}
+	}
+
+	var missingPrompts []string
+	for _, rigName := range rigs {
+		// Check in mayor's clone (canonical for the rig)
+		mayorRig := filepath.Join(ctx.TownRoot, rigName, "mayor", "rig")
+		promptsDir := filepath.Join(mayorRig, "prompts", "roles")
+
+		for _, roleFile := range requiredRolePrompts {
+			promptPath := filepath.Join(promptsDir, roleFile)
+			if _, err := os.Stat(promptPath); os.IsNotExist(err) {
+				missingPrompts = append(missingPrompts, fmt.Sprintf("%s: %s", rigName, roleFile))
+			}
+		}
+	}
+
+	if len(missingPrompts) > 0 {
+		return &CheckResult{
+			Name:    c.Name(),
+			Status:  StatusWarning,
+			Message: fmt.Sprintf("%d role prompt(s) missing", len(missingPrompts)),
+			Details: missingPrompts,
+			FixHint: "Role prompts should be in the project repository under prompts/roles/",
+		}
+	}
+
+	return &CheckResult{
+		Name:    c.Name(),
+		Status:  StatusOK,
+		Message: "All patrol role prompts found",
+	}
+}
diff --git a/internal/rig/manager.go b/internal/rig/manager.go
index 62e5bd18..841c9930 100644
--- a/internal/rig/manager.go
+++ b/internal/rig/manager.go
@@ -283,6 +283,18 @@ func (m *Manager) AddRig(opts AddRigOptions) (*Rig, error) {
 		return nil, fmt.Errorf("initializing wisp beads: %w", err)
 	}
 
+	// Seed patrol molecules for this rig
+	if err := m.seedPatrolMolecules(rigPath); err != nil {
+		// Non-fatal: log warning but continue
+		fmt.Printf("  Warning: Could not seed patrol molecules: %v\n", err)
+	}
+
+	// Create plugin directories
+	if err := m.createPluginDirectories(rigPath); err != nil {
+		// Non-fatal: log warning but continue
+		fmt.Printf("  Warning: Could not create plugin directories: %v\n", err)
+	}
+
 	// Register in town config
 	m.config.Rigs[opts.Name] = config.RigEntry{
 		GitURL:  opts.GitURL,
@@ -491,3 +503,112 @@ func (m *Manager) createRoleCLAUDEmd(workspacePath string, role string, rigName
 	claudePath := filepath.Join(workspacePath, "CLAUDE.md")
 	return os.WriteFile(claudePath, []byte(content), 0644)
 }
+
+// seedPatrolMolecules creates patrol molecule prototypes in the rig's beads database.
+// These molecules define the work loops for Deacon, Witness, and Refinery roles.
+func (m *Manager) seedPatrolMolecules(rigPath string) error {
+	// Use bd command to seed molecules (more reliable than internal API)
+	// The bd mol seed command creates built-in molecules if they don't exist
+	cmd := exec.Command("bd", "mol", "seed", "--patrol")
+	cmd.Dir = rigPath
+	if err := cmd.Run(); err != nil {
+		// Fallback: bd mol seed might not support --patrol yet
+		// Try creating them individually via bd create
+		return m.seedPatrolMoleculesManually(rigPath)
+	}
+	return nil
+}
+
+// seedPatrolMoleculesManually creates patrol molecules using bd create commands.
+func (m *Manager) seedPatrolMoleculesManually(rigPath string) error {
+	// Patrol molecule definitions (subset of builtin_molecules.go for seeding)
+	patrolMols := []struct {
+		title string
+		desc  string
+	}{
+		{
+			title: "Deacon Patrol",
+			desc:  "Mayor's daemon patrol loop for handling callbacks, health checks, and cleanup.",
+		},
+		{
+			title: "Witness Patrol",
+			desc:  "Per-rig worker monitor patrol loop with progressive nudging.",
+		},
+		{
+			title: "Refinery Patrol",
+			desc:  "Merge queue processor patrol loop with verification gates.",
+		},
+	}
+
+	for _, mol := range patrolMols {
+		// Check if already exists by title
+		checkCmd := exec.Command("bd", "list", "--type=molecule", "--format=json")
+		checkCmd.Dir = rigPath
+		output, _ := checkCmd.Output()
+		if strings.Contains(string(output), mol.title) {
+			continue // Already exists
+		}
+
+		// Create the molecule
+		cmd := exec.Command("bd", "create",
+			"--type=molecule",
+			"--title="+mol.title,
+			"--description="+mol.desc,
+			"--priority=2",
+		)
+		cmd.Dir = rigPath
+		if err := cmd.Run(); err != nil {
+			// Non-fatal, continue with others
+			continue
+		}
+	}
+	return nil
+}
+
+// createPluginDirectories creates plugin directories at town and rig levels.
+// - ~/gt/plugins/ (town-level, shared across all rigs)
+// - <rig>/plugins/ (rig-level, rig-specific plugins)
+func (m *Manager) createPluginDirectories(rigPath string) error {
+	// Town-level plugins directory
+	townPluginsDir := filepath.Join(m.townRoot, "plugins")
+	if err := os.MkdirAll(townPluginsDir, 0755); err != nil {
+		return fmt.Errorf("creating town plugins directory: %w", err)
+	}
+
+	// Create a README in town plugins if it doesn't exist
+	townReadme := filepath.Join(townPluginsDir, "README.md")
+	if _, err := os.Stat(townReadme); os.IsNotExist(err) {
+		content := `# Gas Town Plugins
+
+This directory contains town-level plugins that run during Deacon patrol cycles.
+
+## Plugin Structure
+
+Each plugin is a directory containing:
+- plugin.md - Plugin definition with YAML frontmatter
+
+## Gate Types
+
+- cooldown: Time since last run (e.g., 24h)
+- cron: Schedule-based (e.g., "0 9 * * *")
+- condition: Metric threshold
+- event: Trigger-based (startup, heartbeat)
+
+See docs/deacon-plugins.md for full documentation.
+`
+		if writeErr := os.WriteFile(townReadme, []byte(content), 0644); writeErr != nil {
+			// Non-fatal
+			return nil
+		}
+	}
+
+	// Rig-level plugins directory
+	rigPluginsDir := filepath.Join(rigPath, "plugins")
+	if err := os.MkdirAll(rigPluginsDir, 0755); err != nil {
+		return fmt.Errorf("creating rig plugins directory: %w", err)
+	}
+
+	// Add plugins/ to rig .gitignore
+	gitignorePath := filepath.Join(rigPath, ".gitignore")
+	return m.ensureGitignoreEntry(gitignorePath, "plugins/")
+}