diff --git a/apps/desktop/e2e/batch-clarify.spec.ts b/apps/desktop/e2e/batch-clarify.spec.ts
index a3280642d5..062a022b59 100644
--- a/apps/desktop/e2e/batch-clarify.spec.ts
+++ b/apps/desktop/e2e/batch-clarify.spec.ts
@@ -15,7 +15,12 @@
 import { expect, test } from './test'
 
 import { type MockBackendFixture, setupMockBackend, waitForAppReady } from './fixtures'
-import { BATCH_CLARIFY_QUESTIONS, BATCH_CLARIFY_TRIGGER } from '../../../tests-js/scripts/mock-server'
+import {
+  BATCH_CLARIFY_QUESTIONS,
+  BATCH_CLARIFY_TRIGGER,
+  SINGLE_BATCH_CLARIFY_QUESTIONS,
+  SINGLE_BATCH_CLARIFY_TRIGGER
+} from '../../../tests-js/scripts/mock-server'
 
 let fixture: MockBackendFixture | null = null
 
@@ -82,4 +87,40 @@ test.describe('batch clarify card', () => {
     // And still no duplicate live card lingering after settle.
     await expect(page.locator('form[data-clarify-batch]')).toHaveCount(0)
   })
+
+  // #98645: since the questions[]-only schema (#95907) a single question is a
+  // one-entry batch on both the tool args and the gateway wire. The card must
+  // mount and answer exactly like the 2+ case — a blank or spinner-only
+  // section that eats the 10-minute tool timeout is the reported failure.
+  test('renders and answers a one-entry batch like the 2+ case', async () => {
+    const page = fixture!.page
+    const composer = page.locator('[contenteditable="true"]').first()
+    await composer.waitFor({ state: 'visible', timeout: 10_000 })
+
+    await composer.click()
+    await composer.type(SINGLE_BATCH_CLARIFY_TRIGGER, { delay: 20 })
+    await page.keyboard.press('Enter')
+
+    const batchCard = page.locator('form[data-clarify-batch]')
+    await batchCard.first().waitFor({ state: 'visible', timeout: 60_000 })
+
+    await expect(batchCard).toHaveCount(1)
+    await expect(batchCard).toHaveAttribute('data-clarify-batch', '1')
+
+    await expect(batchCard.getByText(SINGLE_BATCH_CLARIFY_QUESTIONS[0]!.question)).toHaveCount(1)
+
+    const confirmButton = batchCard.locator('button[type="submit"]')
+    await expect(confirmButton).toBeDisabled()
+
+    await batchCard.getByRole('button', { name: /Espresso/ }).click()
+    await expect(confirmButton).toBeEnabled()
+    await confirmButton.click()
+
+    const settled = page.locator('[data-clarify-settled]')
+    await settled.waitFor({ state: 'visible', timeout: 30_000 })
+    await expect(settled.getByText(SINGLE_BATCH_CLARIFY_QUESTIONS[0]!.question)).toBeVisible()
+    await expect(settled.getByText('Espresso', { exact: true })).toBeVisible()
+
+    await expect(page.locator('form[data-clarify-batch]')).toHaveCount(0)
+  })
 })
diff --git a/apps/desktop/src/components/assistant-ui/clarify-tool.test.tsx b/apps/desktop/src/components/assistant-ui/clarify-tool.test.tsx
index c5b8ed4486..b6d46bb00a 100644
--- a/apps/desktop/src/components/assistant-ui/clarify-tool.test.tsx
+++ b/apps/desktop/src/components/assistant-ui/clarify-tool.test.tsx
@@ -933,6 +933,107 @@ describe('ClarifyTool batch card', () => {
     expect(request).not.toHaveBeenCalled()
   })
 
+  // ─── Single-entry batch (one-question questions[]) ────────────────────────
+  // #95907 made `questions[]` the only advertised shape, so a single question
+  // now arrives as a one-entry batch on BOTH sides: tool args carry
+  // `questions:[{question, choices}]` and the gateway wire carries
+  // `questions:[{qid, question, choices}]` with no top-level question. The
+  // batch card must mount for the one-entry case exactly as it does for 2+.
+
+  function singleBatchArgs(): { questions: { question: string; choices: string[] }[] } {
+    return {
+      questions: [
+        {
+          choices: ['Local Markdown under .scratch/', 'GitHub Issues', 'Linear', 'GitLab Issues'],
+          question: 'Which issue tracker should this repository use?'
+        }
+      ]
+    }
+  }
+
+  function liveSingleBatchProps(): ToolCallMessagePartProps {
+    const args = singleBatchArgs()
+
+    return {
+      addResult: vi.fn(),
+      args,
+      argsText: JSON.stringify(args),
+      isError: false,
+      respondToApproval: vi.fn(),
+      result: undefined,
+      resume: vi.fn(),
+      status: { type: 'running' },
+      toolCallId: 'clarify-single-batch',
+      toolName: 'clarify',
+      type: 'tool-call'
+    }
+  }
+
+  function singleBatchRequest() {
+    return {
+      choices: null,
+      multiSelect: false,
+      question: '',
+      questions: [
+        {
+          choices: ['Local Markdown under .scratch/', 'GitHub Issues', 'Linear', 'GitLab Issues'],
+          multiSelect: false,
+          qid: 'q0',
+          question: 'Which issue tracker should this repository use?'
+        }
+      ],
+      requestId: 'request-single-batch',
+      sessionId: 'session-1'
+    }
+  }
+
+  it('renders a one-entry batch as the batch card, not a blank/spinner single card', () => {
+    const request = vi.fn().mockResolvedValue({ ok: true, remaining: [] })
+
+    $activeSessionId.set('session-1')
+    $gateway.set({ request } as never)
+    setClarifyRequest(singleBatchRequest())
+    renderClarify(<ClarifyTool {...liveSingleBatchProps()} />)
+
+    expect(screen.getByText('Which issue tracker should this repository use?')).toBeTruthy()
+    expect(screen.getByRole('button', { name: /GitHub Issues/ })).toBeTruthy()
+    expect(document.querySelector('form[data-clarify-batch]')?.getAttribute('data-clarify-batch')).toBe('1')
+  })
+
+  it('mounts the batch card once the wire request lands after the tool row (#98645 timing)', async () => {
+    const request = vi.fn().mockResolvedValue({ ok: true, remaining: [] })
+
+    $activeSessionId.set('session-1')
+    $gateway.set({ request } as never)
+
+    // Tool row mounts FIRST with the model's args; the gateway wire (with the
+    // qid the renderer needs) arrives a beat later — same ordering as
+    // tool.start → clarify.request in a live session.
+    const { rerender } = renderClarify(<ClarifyTool {...liveSingleBatchProps()} />)
+
+    await act(async () => {
+      setClarifyRequest(singleBatchRequest())
+    })
+    rerender(clarifyTree(<ClarifyTool {...liveSingleBatchProps()} />))
+
+    await waitFor(() => {
+      expect(screen.getByText('Which issue tracker should this repository use?')).toBeTruthy()
+    })
+    expect(screen.getByRole('button', { name: /GitHub Issues/ })).toBeTruthy()
+
+    // And the single pick answers with the qid-keyed lock.
+    fireEvent.click(screen.getByRole('button', { name: /GitHub Issues/ }))
+    fireEvent.click(screen.getByRole('button', { name: /Confirm and continue/ }))
+
+    await waitFor(() => {
+      expect(request).toHaveBeenCalledWith('clarify.lock', {
+        answer: 'GitHub Issues',
+        question_id: 'q0',
+        request_id: 'request-single-batch'
+      })
+    })
+  })
+
   it('renders the settled batch with all questions and answers', () => {
     renderClarify(
       <ClarifyTool
diff --git a/tests-js/scripts/mock-server.ts b/tests-js/scripts/mock-server.ts
index 6d1d62eff5..efe9106e8c 100644
--- a/tests-js/scripts/mock-server.ts
+++ b/tests-js/scripts/mock-server.ts
@@ -400,6 +400,22 @@ const BATCH_CLARIFY_TURN: ScriptedTurn = {
   toolCalls: [{ name: 'clarify', args: { questions: BATCH_CLARIFY_QUESTIONS } }],
 }
 
+/**
+ * A marker that makes the mock emit a ONE-ENTRY batch clarify — the exact
+ * payload shape every single question takes since the `questions[]`-only
+ * schema (#95907). Coverage gap called out in #98645: nothing exercised
+ * `questions:[{question, choices}]` before this.
+ */
+export const SINGLE_BATCH_CLARIFY_TRIGGER = 'E2E_SINGLE_BATCH_CLARIFY_TRIGGER'
+export const SINGLE_BATCH_CLARIFY_QUESTIONS = [
+  { question: 'Pick a single-batch drink?', choices: ['Espresso', 'Latte'] },
+]
+
+const SINGLE_BATCH_CLARIFY_TURN: ScriptedTurn = {
+  text: '',
+  toolCalls: [{ name: 'clarify', args: { questions: SINGLE_BATCH_CLARIFY_QUESTIONS } }],
+}
+
 function includesBatchClarifyTrigger(value: unknown): boolean {
   if (typeof value === 'string') {
     return value.includes(BATCH_CLARIFY_TRIGGER)
@@ -416,6 +432,22 @@ function includesBatchClarifyTrigger(value: unknown): boolean {
   return false
 }
 
+function includesSingleBatchClarifyTrigger(value: unknown): boolean {
+  if (typeof value === 'string') {
+    return value.includes(SINGLE_BATCH_CLARIFY_TRIGGER)
+  }
+
+  if (Array.isArray(value)) {
+    return value.some(includesSingleBatchClarifyTrigger)
+  }
+
+  if (value && typeof value === 'object') {
+    return Object.values(value).some(includesSingleBatchClarifyTrigger)
+  }
+
+  return false
+}
+
 /**
  * A marker that makes the mock run a recursive delete through the real
  * `terminal` tool. Under `approvals: mode: "manual"` the backend parks the
@@ -763,6 +795,27 @@ export function startMockServer(options: MockServerOptions = {}): Promise<MockSe
             }
           }
 
+          if (includesSingleBatchClarifyTrigger(parsed.messages)) {
+            // Unlike the 2-question trigger (fresh conversation), this one
+            // shares history with it, so "any tool result" would false-positive
+            // — match only THIS turn's answered result by its question text.
+            const hasOwnToolResult = Array.isArray(parsed.messages)
+              && parsed.messages.some(
+                (message: { role?: string }) =>
+                  message?.role === 'tool' && JSON.stringify(message).includes('single-batch'),
+              )
+
+            if (!hasOwnToolResult) {
+              if (stream) {
+                streamScriptedTurn(res, model, SINGLE_BATCH_CLARIFY_TURN)
+              } else {
+                nonStreamingScriptedTurn(res, model, SINGLE_BATCH_CLARIFY_TURN)
+              }
+
+              return
+            }
+          }
+
           if (includesBlockingClarifyTrigger(parsed.messages)) {
             if (stream) {
               streamScriptedTurn(res, model, BLOCKING_CLARIFY_TURN)