diff --git a/src/components/fragments/FragmentEditor.tsx b/src/components/fragments/FragmentEditor.tsx
index 2acf5932..469fe7bf 100644
--- a/src/components/fragments/FragmentEditor.tsx
+++ b/src/components/fragments/FragmentEditor.tsx
@@ -13,6 +13,7 @@ import type { FrozenSection } from '@/lib/api/types'
 import { RefinementPanel } from '@/components/refinement/RefinementPanel'
 import { copyFragmentToClipboard } from '@/lib/fragment-clipboard'
 import { CropDialog } from '@/components/fragments/CropDialog'
+import { useConfirm } from '@/components/ui/confirm-dialog'
 import { Hint, EmptyHint, MetaLabel } from '@/components/ui/prose-text'
 
 export interface FragmentPrefill {
@@ -37,6 +38,7 @@ export function FragmentEditor({
   onSaved,
 }: FragmentEditorProps) {
   const queryClient = useQueryClient()
+  const confirm = useConfirm()
   const [name, setName] = useState('')
   const [description, setDescription] = useState('')
   const [content, setContent] = useState('')
@@ -541,8 +543,8 @@ export function FragmentEditor({
                   size="sm"
                   variant="ghost"
                   className="h-7 text-xs gap-1 text-muted-foreground hover:text-foreground"
-                  onClick={() => {
-                    if (confirm('Archive this fragment?')) {
+                  onClick={async () => {
+                    if (await confirm({ title: 'Archive this fragment?', confirmText: 'Archive' })) {
                       archiveMutation.mutate()
                     }
                   }}
@@ -578,8 +580,8 @@ export function FragmentEditor({
                     size="sm"
                     variant="ghost"
                     className="h-7 text-xs gap-1 text-destructive/70 hover:text-destructive"
-                    onClick={() => {
-                      if (confirm('Permanently delete this fragment? This cannot be undone.')) {
+                    onClick={async () => {
+                      if (await confirm({ title: 'Permanently delete this fragment?', description: 'This cannot be undone.', confirmText: 'Delete', destructive: true })) {
                         deleteMutation.mutate()
                       }
                     }}
diff --git a/src/components/prose/ProseBlock.tsx b/src/components/prose/ProseBlock.tsx
index 2d108c10..17caaf8e 100644
--- a/src/components/prose/ProseBlock.tsx
+++ b/src/components/prose/ProseBlock.tsx
@@ -11,6 +11,7 @@ import { type ThoughtStep } from './InlineGenerationInput'
 import { buildAnnotationHighlighter, formatDialogue, composeTextTransforms, stripEmphasisInDialogue, type Annotation } from '@/lib/character-mentions'
 import { RefreshCw, Undo2, PenLine, Bug, Trash2, GitBranch, MessageSquare, ChevronLeft, ChevronRight, Info, BookOpen, Volume2, Square } from 'lucide-react'
 import { Caption } from '@/components/ui/prose-text'
+import { useConfirm } from '@/components/ui/confirm-dialog'
 import { useTtsSettings, useIsReadingFragment, playFragment, stopTts } from '@/lib/tts'
 
 interface ProseBlockProps {
@@ -119,6 +120,7 @@ export const ProseBlock = memo(function ProseBlock({
   void isFirst
   void isLast
   const queryClient = useQueryClient()
+  const confirm = useConfirm()
   const [actionMode, setActionMode] = useState<'regenerate' | null>(null)
   const [showUndo, setShowUndo] = useState(false)
   const [isStreamingAction, setIsStreamingAction] = useState(false)
@@ -693,8 +695,8 @@ export const ProseBlock = memo(function ProseBlock({
                     <button
                       className="p-1 rounded-md text-muted-foreground/50 hover:text-destructive hover:bg-destructive/10 transition-all disabled:opacity-25"
                       disabled={deleteMutation.isPending}
-                      onClick={() => {
-                        if (window.confirm('Remove this passage? It will be archived.')) {
+                      onClick={async () => {
+                        if (await confirm({ title: 'Remove this passage?', description: 'It will be archived.', confirmText: 'Remove', destructive: true })) {
                           deleteMutation.mutate()
                           setShowActions(false)
                         }
diff --git a/src/components/prose/TimelineTabs.tsx b/src/components/prose/TimelineTabs.tsx
index 2af46c1f..5c493d49 100644
--- a/src/components/prose/TimelineTabs.tsx
+++ b/src/components/prose/TimelineTabs.tsx
@@ -9,6 +9,7 @@ import {
   DropdownMenuTrigger,
 } from '@/components/ui/dropdown-menu'
 import { GitBranch, Plus, MoreVertical, Pencil, Trash2, EyeOff } from 'lucide-react'
+import { useConfirm } from '@/components/ui/confirm-dialog'
 
 interface TimelineTabsProps {
   storyId: string
@@ -19,6 +20,7 @@ interface TimelineTabsProps {
 
 export function TimelineTabs({ storyId, branches, activeBranchId, onHide }: TimelineTabsProps) {
   const queryClient = useQueryClient()
+  const confirm = useConfirm()
   const [renamingId, setRenamingId] = useState<string | null>(null)
   const [renameValue, setRenameValue] = useState('')
   const [creatingTimeline, setCreatingTimeline] = useState(false)
@@ -126,8 +128,8 @@ export function TimelineTabs({ storyId, branches, activeBranchId, onHide }: Time
                   {!isMain && (
                     <DropdownMenuItem
                       className="text-destructive focus:text-destructive"
-                      onClick={() => {
-                        if (window.confirm(`Delete timeline "${branch.name}"? This cannot be undone.`)) {
+                      onClick={async () => {
+                        if (await confirm({ title: `Delete timeline "${branch.name}"?`, description: 'This cannot be undone.', confirmText: 'Delete', destructive: true })) {
                           deleteMutation.mutate(branch.id)
                         }
                       }}
diff --git a/src/components/sidebar/ArchivePanel.tsx b/src/components/sidebar/ArchivePanel.tsx
index f77a17b6..88757f6c 100644
--- a/src/components/sidebar/ArchivePanel.tsx
+++ b/src/components/sidebar/ArchivePanel.tsx
@@ -8,6 +8,7 @@ import { ScrollArea } from '@/components/ui/scroll-area'
 import { Spinner, EmptyState } from '@/components/ui/async-view'
 import { Undo2, Trash2, Archive } from 'lucide-react'
 import { componentId } from '@/lib/dom-ids'
+import { useConfirm } from '@/components/ui/confirm-dialog'
 
 interface ArchivePanelProps {
   storyId: string
@@ -16,6 +17,7 @@ interface ArchivePanelProps {
 
 export function ArchivePanel({ storyId, onSelect }: ArchivePanelProps) {
   const queryClient = useQueryClient()
+  const confirm = useConfirm()
   const [search, setSearch] = useState('')
 
   const { data: archivedFragments, isLoading } = useQuery({
@@ -118,9 +120,9 @@ export function ArchivePanel({ storyId, onSelect }: ArchivePanelProps) {
                   size="icon"
                   variant="ghost"
                   className="size-7 text-muted-foreground hover:text-destructive"
-                  onClick={(e) => {
+                  onClick={async (e) => {
                     e.stopPropagation()
-                    if (confirm('Permanently delete this fragment? This cannot be undone.')) {
+                    if (await confirm({ title: 'Permanently delete this fragment?', description: 'This cannot be undone.', confirmText: 'Delete', destructive: true })) {
                       deleteMutation.mutate(fragment.id)
                     }
                   }}
diff --git a/src/components/sidebar/TimelineManagerPanel.tsx b/src/components/sidebar/TimelineManagerPanel.tsx
index 31f6949c..f4d21104 100644
--- a/src/components/sidebar/TimelineManagerPanel.tsx
+++ b/src/components/sidebar/TimelineManagerPanel.tsx
@@ -5,6 +5,7 @@ import { Button } from '@/components/ui/button'
 import { ScrollArea } from '@/components/ui/scroll-area'
 import { GitBranch, Plus, Pencil, Trash2, Check, X } from 'lucide-react'
 import { MetaLabel } from '@/components/ui/prose-text'
+import { useConfirm } from '@/components/ui/confirm-dialog'
 
 interface TimelineManagerPanelProps {
   storyId: string
@@ -12,6 +13,7 @@ interface TimelineManagerPanelProps {
 
 export function TimelineManagerPanel({ storyId }: TimelineManagerPanelProps) {
   const queryClient = useQueryClient()
+  const confirm = useConfirm()
   const [creatingTimeline, setCreatingTimeline] = useState(false)
   const [newTimelineName, setNewTimelineName] = useState('')
   const [renamingId, setRenamingId] = useState<string | null>(null)
@@ -206,8 +208,8 @@ export function TimelineManagerPanel({ storyId }: TimelineManagerPanelProps) {
                   {!isMain && (
                     <button
                       className="p-1 rounded text-muted-foreground hover:text-destructive hover:bg-destructive/10 transition-all"
-                      onClick={() => {
-                        if (window.confirm(`Delete timeline "${branch.name}"?`)) {
+                      onClick={async () => {
+                        if (await confirm({ title: `Delete timeline "${branch.name}"?`, description: 'This cannot be undone.', confirmText: 'Delete', destructive: true })) {
                           deleteMutation.mutate(branch.id)
                         }
                       }}
diff --git a/src/components/ui/confirm-dialog.tsx b/src/components/ui/confirm-dialog.tsx
new file mode 100644
index 00000000..880cc013
--- /dev/null
+++ b/src/components/ui/confirm-dialog.tsx
@@ -0,0 +1,80 @@
+import { createContext, useCallback, useContext, useRef, useState } from 'react'
+import {
+  Dialog,
+  DialogContent,
+  DialogDescription,
+  DialogFooter,
+  DialogHeader,
+  DialogTitle,
+} from '@/components/ui/dialog'
+import { Button } from '@/components/ui/button'
+
+export interface ConfirmOptions {
+  title: string
+  description?: string
+  confirmText?: string
+  cancelText?: string
+  /** Style the confirm button as a destructive action. */
+  destructive?: boolean
+}
+
+type ConfirmFn = (options: ConfirmOptions) => Promise<boolean>
+
+const ConfirmContext = createContext<ConfirmFn | null>(null)
+
+/**
+ * Async confirm() resolving true/false — use instead of native window.confirm(), which
+ * on Electron can leave the window unfocused (blocking input) after it closes.
+ */
+export function useConfirm(): ConfirmFn {
+  const ctx = useContext(ConfirmContext)
+  if (!ctx) throw new Error('useConfirm must be used within a ConfirmProvider')
+  return ctx
+}
+
+export function ConfirmProvider({ children }: { children: React.ReactNode }) {
+  const [options, setOptions] = useState<ConfirmOptions | null>(null)
+  const resolverRef = useRef<((value: boolean) => void) | null>(null)
+
+  const confirm = useCallback<ConfirmFn>((opts) => {
+    setOptions(opts)
+    return new Promise<boolean>((resolve) => {
+      resolverRef.current = resolve
+    })
+  }, [])
+
+  const settle = useCallback((result: boolean) => {
+    resolverRef.current?.(result)
+    resolverRef.current = null
+    setOptions(null)
+  }, [])
+
+  return (
+    <ConfirmContext.Provider value={confirm}>
+      {children}
+      <Dialog open={options !== null} onOpenChange={(open) => { if (!open) settle(false) }}>
+        {options && (
+          <DialogContent showCloseButton={false} className="sm:max-w-sm">
+            <DialogHeader>
+              <DialogTitle>{options.title}</DialogTitle>
+              {options.description && (
+                <DialogDescription>{options.description}</DialogDescription>
+              )}
+            </DialogHeader>
+            <DialogFooter>
+              <Button variant="ghost" onClick={() => settle(false)}>
+                {options.cancelText ?? 'Cancel'}
+              </Button>
+              <Button
+                variant={options.destructive ? 'destructive' : 'default'}
+                onClick={() => settle(true)}
+              >
+                {options.confirmText ?? 'Confirm'}
+              </Button>
+            </DialogFooter>
+          </DialogContent>
+        )}
+      </Dialog>
+    </ConfirmContext.Provider>
+  )
+}
diff --git a/src/routes/__root.tsx b/src/routes/__root.tsx
index ea0c9e8d..4c6d16d4 100644
--- a/src/routes/__root.tsx
+++ b/src/routes/__root.tsx
@@ -6,6 +6,7 @@ import {
 } from '@tanstack/react-router'
 import { QueryClient, QueryClientProvider } from '@tanstack/react-query'
 import { TooltipProvider } from '@/components/ui/tooltip'
+import { ConfirmProvider } from '@/components/ui/confirm-dialog'
 import { ThemeProvider } from '@/lib/theme'
 import { HelpProvider } from '@/hooks/use-help'
 import { HelpPanel } from '@/components/help/HelpPanel'
@@ -111,12 +112,14 @@ function RootComponent() {
       <CustomCssProvider />
       <QueryClientProvider client={queryClient}>
         <TooltipProvider>
-          <HelpProvider>
-            <Outlet />
-            <HelpPanel />
-            <TtsPlayerBar />
-            <DesktopUpdateBanner />
-          </HelpProvider>
+          <ConfirmProvider>
+            <HelpProvider>
+              <Outlet />
+              <HelpPanel />
+              <TtsPlayerBar />
+              <DesktopUpdateBanner />
+            </HelpProvider>
+          </ConfirmProvider>
         </TooltipProvider>
       </QueryClientProvider>
     </ThemeProvider>
diff --git a/src/routes/index.tsx b/src/routes/index.tsx
index d8219949..42f906e1 100644
--- a/src/routes/index.tsx
+++ b/src/routes/index.tsx
@@ -38,6 +38,7 @@ import { ProviderList, ProviderPanel } from '@/components/settings/ProviderManag
 import { AboutSection } from '@/components/settings/AboutPanel'
 import { DesktopUpdatesControls } from '@/components/settings/DesktopUpdatesPanel'
 import { SectionHeading } from '@/components/settings/primitives'
+import { useConfirm } from '@/components/ui/confirm-dialog'
 
 const THEME_OPTIONS = [
   { value: 'light' as const, label: 'Light', Icon: Sun },
@@ -49,6 +50,7 @@ export const Route = createFileRoute('/')({ component: StoryListPage })
 
 function StoryListPage() {
   const queryClient = useQueryClient()
+  const confirm = useConfirm()
   const navigate = useNavigate()
   const { theme, setTheme } = useTheme()
   const [open, setOpen] = useState(false)
@@ -661,8 +663,8 @@ function StoryListPage() {
               key={story.id}
               story={story}
               isRecent={i === 0 && sortedStories.length > 1}
-              onDelete={() => {
-                if (confirm(`Delete "${story.name}"?`)) {
+              onDelete={async () => {
+                if (await confirm({ title: `Delete "${story.name}"?`, description: 'This permanently deletes the story and all its fragments.', confirmText: 'Delete', destructive: true })) {
                   deleteMutation.mutate(story.id)
                 }
               }}