diff --git a/cmd/sync.go b/cmd/sync.go
index 56e5705..a2af5a2 100644
--- a/cmd/sync.go
+++ b/cmd/sync.go
@@ -4,6 +4,7 @@ import (
 	"bufio"
 	"errors"
 	"fmt"
+	"io"
 	"os"
 	"strings"
 	"sync"
@@ -22,6 +23,8 @@ var (
 	syncForce  bool
 	syncResume bool
 	syncAbort  bool
+	// stdinReader allows tests to inject mock input for prompts
+	stdinReader io.Reader = os.Stdin
 )
 
 // Git config keys for sync state persistence
@@ -178,7 +181,22 @@ func runSync(gitClient git.GitClient, githubClient github.GitHubClient) error {
 		if hasSavedState {
 			fmt.Fprintf(os.Stderr, "Warning: found state from a previous interrupted sync\n")
 			fmt.Fprintf(os.Stderr, "If you resolved rebase conflicts, run 'stack sync --resume'\n")
-			fmt.Fprintf(os.Stderr, "Otherwise, cleaning up stale state and starting fresh...\n\n")
+			fmt.Fprintf(os.Stderr, "\nStart fresh? [y/N] ")
+
+			reader := bufio.NewReader(stdinReader)
+			input, err := reader.ReadString('\n')
+			if err != nil {
+				return fmt.Errorf("failed to read input: %w", err)
+			}
+
+			input = strings.TrimSpace(strings.ToLower(input))
+			if input != "y" && input != "yes" {
+				fmt.Println("Aborted. Use 'stack sync --resume' or 'stack sync --abort' to handle the interrupted sync.")
+				return nil
+			}
+
+			fmt.Println("Cleaning up stale state and starting fresh...")
+			fmt.Println()
 			// Clean up stale state
 			_ = gitClient.UnsetConfig(configSyncStashed)
 			_ = gitClient.UnsetConfig(configSyncOriginalBranch)
@@ -245,7 +263,7 @@ func runSync(gitClient git.GitClient, githubClient github.GitHubClient) error {
 		fmt.Printf("Branch '%s' is not in a stack.\n", originalBranch)
 		fmt.Printf("Add it with parent '%s'? [Y/n] ", baseBranch)
 
-		reader := bufio.NewReader(os.Stdin)
+		reader := bufio.NewReader(stdinReader)
 		input, err := reader.ReadString('\n')
 		if err != nil {
 			return fmt.Errorf("failed to read input: %w", err)
@@ -510,6 +528,17 @@ func runSync(gitClient git.GitClient, githubClient github.GitHubClient) error {
 		if !stackBranchSet[branch.Parent] {
 			// Parent is not a stack branch, so it's a base branch - use origin/<parent>
 			rebaseTarget = "origin/" + branch.Parent
+
+			// Explicitly fetch the base branch to ensure tracking ref is up to date
+			// This is needed because 'git fetch origin' may not always update tracking refs
+			// reliably (e.g., repos with limited refspecs or certain git configurations)
+			if err := gitClient.FetchBranch(branch.Parent); err != nil {
+				// Non-fatal: continue with potentially stale ref, rebase will still work
+				// but might not include latest changes from the base branch
+				if git.Verbose {
+					fmt.Printf("  Note: could not fetch %s: %v\n", branch.Parent, err)
+				}
+			}
 		}
 
 		// Rebase onto parent
diff --git a/cmd/sync_test.go b/cmd/sync_test.go
index 8f5505f..3f52931 100644
--- a/cmd/sync_test.go
+++ b/cmd/sync_test.go
@@ -2,6 +2,8 @@ package cmd
 
 import (
 	"fmt"
+	"os"
+	"strings"
 	"testing"
 
 	"github.com/javoire/stackinator/internal/github"
@@ -55,6 +57,7 @@ func TestRunSyncBasic(t *testing.T) {
 		mockGit.On("CheckoutBranch", "feature-a").Return(nil)
 		mockGit.On("GetCommitHash", "feature-a").Return("abc123", nil)
 		mockGit.On("GetCommitHash", "origin/feature-a").Return("abc123", nil)
+		mockGit.On("FetchBranch", "main").Return(nil) // Fetch base branch before rebase
 		// Patch-based unique commit detection
 		mockGit.On("GetUniqueCommitsByPatch", "origin/main", "feature-a").Return([]string{"abc123"}, nil)
 		mockGit.On("GetMergeBase", "feature-a", "origin/main").Return("main123", nil)
@@ -141,6 +144,7 @@ func TestRunSyncMergedParent(t *testing.T) {
 		mockGit.On("CheckoutBranch", "feature-b").Return(nil)
 		mockGit.On("GetCommitHash", "feature-b").Return("def456", nil)
 		mockGit.On("GetCommitHash", "origin/feature-b").Return("def456", nil)
+		mockGit.On("FetchBranch", "main").Return(nil) // Fetch base branch before rebase
 		mockGit.On("RebaseOnto", "origin/main", "feature-a", "feature-b").Return(nil)
 		mockGit.On("FetchBranch", "feature-b").Return(nil)
 		mockGit.On("PushWithExpectedRemote", "feature-b", "def456").Return(nil)
@@ -207,6 +211,7 @@ func TestRunSyncUpdatePRBase(t *testing.T) {
 		mockGit.On("CheckoutBranch", "feature-a").Return(nil)
 		mockGit.On("GetCommitHash", "feature-a").Return("abc123", nil)
 		mockGit.On("GetCommitHash", "origin/feature-a").Return("abc123", nil)
+		mockGit.On("FetchBranch", "main").Return(nil) // Fetch base branch before rebase
 		mockGit.On("GetUniqueCommitsByPatch", "origin/main", "feature-a").Return([]string{"abc123"}, nil)
 		mockGit.On("GetMergeBase", "feature-a", "origin/main").Return("main123", nil)
 		mockGit.On("GetCommitHash", "origin/main").Return("main123", nil)
@@ -287,6 +292,7 @@ func TestRunSyncStashHandling(t *testing.T) {
 		mockGit.On("CheckoutBranch", "feature-a").Return(nil)
 		mockGit.On("GetCommitHash", "feature-a").Return("abc123", nil)
 		mockGit.On("GetCommitHash", "origin/feature-a").Return("abc123", nil)
+		mockGit.On("FetchBranch", "main").Return(nil) // Fetch base branch before rebase
 		mockGit.On("GetUniqueCommitsByPatch", "origin/main", "feature-a").Return([]string{"abc123"}, nil)
 		mockGit.On("GetMergeBase", "feature-a", "origin/main").Return("main123", nil)
 		mockGit.On("GetCommitHash", "origin/main").Return("main123", nil)
@@ -347,6 +353,7 @@ func TestRunSyncErrorHandling(t *testing.T) {
 		mockGit.On("CheckoutBranch", "feature-a").Return(nil)
 		mockGit.On("GetCommitHash", "feature-a").Return("abc123", nil)
 		mockGit.On("GetCommitHash", "origin/feature-a").Return("abc123", nil)
+		mockGit.On("FetchBranch", "main").Return(nil) // Fetch base branch before rebase
 		mockGit.On("GetUniqueCommitsByPatch", "origin/main", "feature-a").Return([]string{"abc123"}, nil)
 		mockGit.On("GetMergeBase", "feature-a", "origin/main").Return("main123", nil)
 		mockGit.On("GetCommitHash", "origin/main").Return("main123", nil)
@@ -400,6 +407,7 @@ func TestRunSyncErrorHandling(t *testing.T) {
 		mockGit.On("CheckoutBranch", "feature-a").Return(nil)
 		mockGit.On("GetCommitHash", "feature-a").Return("abc123", nil)
 		mockGit.On("GetCommitHash", "origin/feature-a").Return("abc123", nil)
+		mockGit.On("FetchBranch", "main").Return(nil) // Fetch base branch before rebase
 		mockGit.On("GetUniqueCommitsByPatch", "origin/main", "feature-a").Return([]string{"abc123"}, nil)
 		mockGit.On("GetMergeBase", "feature-a", "origin/main").Return("main123", nil)
 		mockGit.On("GetCommitHash", "origin/main").Return("main123", nil)
@@ -545,6 +553,7 @@ func TestRunSyncResume(t *testing.T) {
 		mockGit.On("CheckoutBranch", "feature-a").Return(nil)
 		mockGit.On("GetCommitHash", "feature-a").Return("abc123", nil)
 		mockGit.On("GetCommitHash", "origin/feature-a").Return("abc123", nil)
+		mockGit.On("FetchBranch", "main").Return(nil) // Fetch base branch before rebase
 		mockGit.On("GetUniqueCommitsByPatch", "origin/main", "feature-a").Return([]string{"abc123"}, nil)
 		mockGit.On("GetMergeBase", "feature-a", "origin/main").Return("main123", nil)
 		mockGit.On("GetCommitHash", "origin/main").Return("main123", nil)
@@ -569,14 +578,18 @@ func TestRunSyncResume(t *testing.T) {
 		mockGH.AssertExpectations(t)
 	})
 
-	t.Run("orphaned state is cleaned up on fresh sync", func(t *testing.T) {
+	t.Run("stale state cleaned up when user confirms", func(t *testing.T) {
 		mockGit := new(testutil.MockGitClient)
 		mockGH := new(testutil.MockGitHubClient)
 
+		// Inject "y" input for the prompt
+		stdinReader = strings.NewReader("y\n")
+		defer func() { stdinReader = os.Stdin }()
+
 		// Orphaned state exists but --resume not passed
 		mockGit.On("GetConfig", "stack.sync.stashed").Return("true")
 		mockGit.On("GetConfig", "stack.sync.originalBranch").Return("old-branch")
-		// Clean up orphaned state
+		// Clean up orphaned state (user confirmed)
 		mockGit.On("UnsetConfig", "stack.sync.stashed").Return(nil)
 		mockGit.On("UnsetConfig", "stack.sync.originalBranch").Return(nil)
 
@@ -607,6 +620,7 @@ func TestRunSyncResume(t *testing.T) {
 		mockGit.On("CheckoutBranch", "feature-a").Return(nil)
 		mockGit.On("GetCommitHash", "feature-a").Return("abc123", nil)
 		mockGit.On("GetCommitHash", "origin/feature-a").Return("abc123", nil)
+		mockGit.On("FetchBranch", "main").Return(nil) // Fetch base branch before rebase
 		mockGit.On("GetUniqueCommitsByPatch", "origin/main", "feature-a").Return([]string{"abc123"}, nil)
 		mockGit.On("GetMergeBase", "feature-a", "origin/main").Return("main123", nil)
 		mockGit.On("GetCommitHash", "origin/main").Return("main123", nil)
@@ -626,6 +640,28 @@ func TestRunSyncResume(t *testing.T) {
 		mockGit.AssertExpectations(t)
 		mockGH.AssertExpectations(t)
 	})
+
+	t.Run("sync aborted when user declines stale state cleanup", func(t *testing.T) {
+		mockGit := new(testutil.MockGitClient)
+		mockGH := new(testutil.MockGitHubClient)
+
+		// Inject "n" input for the prompt (user declines)
+		stdinReader = strings.NewReader("n\n")
+		defer func() { stdinReader = os.Stdin }()
+
+		// Orphaned state exists but --resume not passed
+		mockGit.On("GetConfig", "stack.sync.stashed").Return("true")
+		mockGit.On("GetConfig", "stack.sync.originalBranch").Return("old-branch")
+
+		// User declined, so sync should abort without calling any other methods
+
+		err := runSync(mockGit, mockGH)
+
+		// Should return nil (not an error) since user chose to abort
+		assert.NoError(t, err)
+		mockGit.AssertExpectations(t)
+		mockGH.AssertExpectations(t)
+	})
 }
 
 func TestRunSyncAbort(t *testing.T) {