@@ -23,14 +23,10 @@ import { createMockRequest } from '@sim/testing/mocks/request.mock'
 import { beforeEach, describe, expect, it, vi } from 'vitest'
 
 const {
-  mockBuildSelectedMcpToolSchemas,
-  mockBuildTaggedMcpToolSchemas,
   mockComputeWorkspaceEntitlements,
   mockProcessContextsServer,
   mockRequestExplicitStreamAbort,
 } = vi.hoisted(() => ({
-  mockBuildSelectedMcpToolSchemas: vi.fn(),
-  mockBuildTaggedMcpToolSchemas: vi.fn(),
   mockComputeWorkspaceEntitlements: vi.fn(),
   mockProcessContextsServer: vi.fn(),
   mockRequestExplicitStreamAbort: vi.fn(),
@@ -53,11 +49,6 @@ vi.mock('@/lib/mothership/entitlements', () => ({
   computeWorkspaceEntitlements: mockComputeWorkspaceEntitlements,
 }))
 
-vi.mock('@/lib/mothership/mcp-tools', () => ({
-  buildSelectedMcpToolSchemas: mockBuildSelectedMcpToolSchemas,
-  buildTaggedMcpToolSchemas: mockBuildTaggedMcpToolSchemas,
-}))
-
 vi.mock('@/lib/mothership/request/lifecycle/headless', () => mothershipHeadlessLifecycleMock)
 
 vi.mock('@/lib/mothership/request/session/explicit-abort', () => ({
@@ -144,8 +135,6 @@ describe('mothership private trace provenance transport', () => {
       decryptionFailures: [],
     })
     mockBuildIntegrationToolSchemas.mockResolvedValue([])
-    mockBuildSelectedMcpToolSchemas.mockResolvedValue([])
-    mockBuildTaggedMcpToolSchemas.mockResolvedValue([])
     mockComputeWorkspaceEntitlements.mockResolvedValue([])
     mockDecryptSecret.mockResolvedValue({ decrypted: 'secret-value' })
     mockProcessContextsServer.mockResolvedValue([])
@@ -484,9 +473,6 @@ describe('mothership private trace provenance transport', () => {
   })
 
   it('sends enabled MCP IDs without schemas or activating matching configured secrets', async () => {
-    mockBuildTaggedMcpToolSchemas.mockResolvedValueOnce([
-      { name: 'mcp-docs', description: 'Uses secret-value' },
-    ])
     mockRunHeadlessCopilotLifecycle.mockImplementation(
       async (payload: Record<string, unknown>, options: CopilotLifecycleOptions) => {
         const registry =
 
@@ -112,11 +112,6 @@ permissionGroupsResolveMockFns.mockGetUserPermissionConfigForOrganization.mockIm
 
 vi.mock('@/lib/billing/plan-helpers', () => billingPlanHelpersMock)
 
-vi.mock('@/lib/mothership/mcp-tools', () => ({
-  buildTaggedMcpToolSchemas: vi.fn(async () => []),
-  buildOrganizationTaggedMcpToolSchemas: vi.fn(async () => []),
-}))
-
 vi.mock('@/lib/workflows/utils', () => workflowsUtilsMock)
 
 /** Denied-operation projection walks the block map only for blocks the mocked tool list never names. */
@@ -891,9 +886,7 @@ describe('desktop request capabilities', () => {
 
 it('carries only enabled MCP IDs without eager catalog discovery while preserving desktop capabilities', async () => {
   const { getBlockVisibilityForCopilot } = await import('@/lib/mothership/block-visibility')
-  const { buildOrganizationTaggedMcpToolSchemas } = await import('@/lib/mothership/mcp-tools')
   vi.mocked(getBlockVisibilityForCopilot).mockClear()
-  vi.mocked(buildOrganizationTaggedMcpToolSchemas).mockClear()
   const principal = createSessionPrincipal({ userId: 'user-org' })
   const payload = await buildCopilotRequestPayload({
     message: 'Use my tools',
@@ -909,7 +902,6 @@ it('carries only enabled MCP IDs without eager catalog discovery while preservin
     terminalCapable: true,
   })
   expect(getBlockVisibilityForCopilot).not.toHaveBeenCalled()
-  expect(buildOrganizationTaggedMcpToolSchemas).not.toHaveBeenCalled()
   expect(payload.integrationCatalog).toEqual({ mcpServerIds: ['server-a', 'server-b'] })
   expect(payload).not.toHaveProperty('integrationTools')
   expect(payload).not.toHaveProperty('mothershipTools')
 
@@ -514,11 +514,12 @@ function normalizeContexts(contexts: UnifiedChatRequest['contexts']) {
  * reloads and reopened chats with no extra state to keep in sync. There is
  * deliberately no off switch: history is append-only.
  *
- * Only the ids travel forward, not the contexts themselves. The tools ride the
- * tool array on every turn, so the model always sees their names and schemas;
- * re-expanding the prompt listing each turn would just duplicate that. Keeping
- * inherited servers out of the persisted contexts also keeps the `/name` chips
- * on a sent message showing only what the user actually typed that turn.
+ * Only the ids travel forward, not the contexts themselves. The ids scope the
+ * request's integration catalog, and the agent discovers these servers'
+ * operations on demand, so re-expanding the prompt listing each turn adds
+ * nothing. Keeping inherited servers out of the persisted contexts also keeps
+ * the `/name` chips on a sent message showing only what the user actually typed
+ * that turn.
  */
 function collectChatMcpServerIds(
   chatMcpServerIds: string[],
 
@@ -635,7 +635,7 @@ describe('processContextsServer - MCP contexts', () => {
       },
     ])
     expect(discoverServerTools).not.toHaveBeenCalled()
-    const catalog = await buildTaggedMcpToolSchemas('user-1', 'ws-1', ['mcp-server-1'])
+    const { tools: catalog } = await buildTaggedMcpToolSchemas('user-1', 'ws-1', ['mcp-server-1'])
     expect(discoverServerTools).toHaveBeenCalledTimes(1)
     expect(discoverServerTools).toHaveBeenCalledWith({
       principal: expect.objectContaining({
 
@@ -10,6 +10,10 @@ import {
   mothershipWorkspaceTargetMock,
   mothershipWorkspaceTargetMockFns,
 } from '@sim/testing/mocks/mothership-workspace-target.mock'
+import {
+  permissionCheckMock,
+  permissionCheckMockFns,
+} from '@sim/testing/mocks/permission-check.mock'
 import {
   permissionGroupsResolveMock,
   permissionGroupsResolveMockFns,
@@ -19,6 +23,7 @@ import {
   workspaceContextMockFns,
 } from '@sim/testing/mocks/workspace-context.mock'
 import { beforeEach, describe, expect, it, vi } from 'vitest'
+import { OrchestrationError } from '@/lib/core/orchestration/types'
 import {
   createTrustedCopilotPrincipal,
   createTrustedOrganizationCopilotPrincipal,
@@ -30,9 +35,11 @@ import {
   readIntegrationCatalog,
 } from '@/lib/mothership/integrations/application/catalog'
 
-const hoisted = vi.hoisted(() => ({ mcp: vi.fn(), flag: vi.fn(async () => true) }))
+const hoisted = vi.hoisted(() => ({ flag: vi.fn(async () => true) }))
 const mocks = {
   ...hoisted,
+  discover: mcpUseCasesMockFns.mockDiscoverMcpServerToolsUseCase,
+  mcpPermission: permissionCheckMockFns.mockAssertPermissionsAllowed,
   build: mothershipChatPayloadMockFns.mockBuildIntegrationToolSchemas,
   banned: authBanMockFns.mockGetActivelyBannedUserIds,
   target: mothershipWorkspaceTargetMockFns.mockResolveInvocationWorkspace,
@@ -42,7 +49,8 @@ const mocks = {
 }
 vi.mock('@/lib/mcp/application/use-cases', () => mcpUseCasesMock)
 vi.mock('@/lib/mothership/chat/payload', () => mothershipChatPayloadMock)
-vi.mock('@/lib/mothership/mcp-tools', () => ({ buildTaggedMcpToolSchemas: hoisted.mcp }))
+vi.mock('@/lib/internal/mcp/discover-tools', () => ({ discoverMcpServerToolsAsExecutor: vi.fn() }))
+vi.mock('@/ee/access-control/utils/permission-check', () => permissionCheckMock)
 vi.mock('@/lib/mothership/application/workspace-target', () => mothershipWorkspaceTargetMock)
 vi.mock('@/lib/workspaces/application/context', () => workspaceContextMock)
 vi.mock('@/lib/auth/ban', () => authBanMock)
@@ -64,6 +72,9 @@ const tools = [
     input_schema: { type: 'object' },
   },
 ]
+function discoveredServerIds() {
+  return mocks.discover.mock.calls.map(([args]) => args.input.serverId)
+}
 function principal() {
   return createTrustedOrganizationCopilotPrincipal(
     { userId: 'actor', organizationId: 'org-1', chatId: 'chat-1', delegationId: 'catalog-1' },
@@ -82,7 +93,9 @@ beforeEach(() => {
   mocks.banned.mockResolvedValue([])
   mocks.config.mockResolvedValue(null)
   mocks.build.mockResolvedValue([...tools])
-  mocks.mcp.mockResolvedValue([])
+  mocks.discover.mockReset()
+  mocks.discover.mockResolvedValue({ tools: [] })
+  mocks.mcpPermission.mockResolvedValue(undefined)
   mocks.listServers.mockResolvedValue({ servers: [{ id: 'mcp-abc' }] })
 })
 describe('integration catalog projection', () => {
@@ -238,7 +251,9 @@ describe('catalog authorization', () => {
 
   it('does not discover MCP operations in Search even with selected servers', async () => {
     queueChat()
-    mocks.mcp.mockResolvedValue([{ ...tools[0], name: 'mcp-abc-send', service: 'mcp:mcp-abc' }])
+    mocks.discover.mockResolvedValue({
+      tools: [{ serverId: 'mcp-abc', name: 'send', description: 'Send', inputSchema: {} }],
+    })
     const result = await readIntegrationCatalog.execute({
       principal: principal(),
       input: { ...input, service: 'mcp:mcp-abc', mcpServerIds: ['mcp-abc'] },
@@ -297,10 +312,12 @@ it.each([undefined, 'mcp-abc-write'])(
   async (toolId) => {
     queueChat('agent')
     mocks.target.mockResolvedValue({ workspaceId: 'workspace-1' })
-    mocks.mcp.mockResolvedValue([
-      { name: 'mcp-abc-read', service: 'mcp:mcp-abc', description: 'Read', input_schema: {} },
-      { name: 'mcp-abc-write', service: 'mcp:mcp-abc', description: 'Write', input_schema: {} },
-    ])
+    mocks.discover.mockResolvedValue({
+      tools: [
+        { serverId: 'mcp-abc', name: 'read', description: 'Read', inputSchema: {} },
+        { serverId: 'mcp-abc', name: 'write', description: 'Write', inputSchema: {} },
+      ],
+    })
     const result = await readIntegrationCatalog.execute({
       principal: principal(),
       input: {
@@ -312,7 +329,7 @@ it.each([undefined, 'mcp-abc-write'])(
         ...(toolId ? { toolId } : {}),
       },
     })
-    expect(mocks.mcp).toHaveBeenCalledWith('actor', 'workspace-1', ['mcp-abc'], undefined)
+    expect(discoveredServerIds()).toEqual(['mcp-abc'])
     expect(result.operations.map((operation) => operation.toolId)).toEqual(
       toolId ? [] : ['mcp-abc-read']
     )
@@ -325,7 +342,7 @@ it('keeps native discovery available in organization chats with tagged MCP serve
     input: { ...input, mode: 'agent', mcpServerIds: ['mcp-abc'], toolId: 'gmail_send' },
   })
   expect(result.operations.map((operation) => operation.toolId)).toEqual(['gmail_send'])
-  expect(mocks.mcp).not.toHaveBeenCalled()
+  expect(mocks.discover).not.toHaveBeenCalled()
 })
 it('requires an explicit workspace target for organization MCP discovery', async () => {
   queueChat('agent')
@@ -335,7 +352,7 @@ it('requires an explicit workspace target for organization MCP discovery', async
       input: { ...input, mode: 'agent', mcpServerIds: ['mcp-abc'], toolId: 'mcp-abc-read' },
     })
   ).rejects.toThrow('explicit workspace ID')
-  expect(mocks.mcp).not.toHaveBeenCalled()
+  expect(mocks.discover).not.toHaveBeenCalled()
 })
 
 it('ranks query tokens across operation names, descriptions, and service while prioritizing exact IDs', () => {
@@ -381,7 +398,7 @@ it('filters organization enabled servers to the authorized target before broad M
     principal: expect.objectContaining({ workspaceId: 'workspace-1', subjectUserId: 'actor' }),
     input: { workspaceId: 'workspace-1' },
   })
-  expect(mocks.mcp).toHaveBeenCalledWith('actor', 'workspace-1', ['mcp-abc'], undefined)
+  expect(discoveredServerIds()).toEqual(['mcp-abc'])
 })
 
 it('removes previously discoverable Search operations when the runtime flag turns off', async () => {
@@ -394,3 +411,59 @@ it('removes previously discoverable Search operations when the runtime flag turn
     )
   }
 })
+
+describe('tagged MCP servers that cannot be discovered', () => {
+  const failures: Record<string, () => Promise<never> | Promise<{ tools: never[] }>> = {
+    'mcp-deleted': async () => {
+      throw new OrchestrationError('not_found', 'MCP server not found')
+    },
+    'mcp-down': async () => {
+      throw new Error('connect ECONNREFUSED')
+    },
+    'mcp-empty': async () => ({ tools: [] }),
+  }
+  const serverIds = ['mcp-abc', ...Object.keys(failures)]
+  function catalog(request: Partial<IntegrationCatalogRequest>) {
+    queueChat('agent')
+    return readIntegrationCatalog.execute({
+      principal: principal(),
+      input: {
+        ...input,
+        mode: 'agent',
+        workspaceId: 'workspace-1',
+        mcpServerIds: serverIds,
+        ...request,
+      },
+    })
+  }
+  beforeEach(() => {
+    mocks.target.mockResolvedValue({ workspaceId: 'workspace-1' })
+    mocks.listServers.mockResolvedValue({ servers: serverIds.map((id) => ({ id })) })
+    mocks.discover.mockImplementation(async ({ input: { serverId } }) => {
+      const failure = failures[serverId]
+      if (failure) return failure()
+      return { tools: [{ serverId, name: 'send', description: 'Send a note', inputSchema: {} }] }
+    })
+  })
+
+  it.each([undefined, 'send'])(
+    'still lists native and healthy MCP operations (query: %s)',
+    async (query) => {
+      const result = await catalog(query ? { query } : {})
+      expect(result.operations.map((operation) => operation.toolId)).toEqual(
+        expect.arrayContaining(['gmail_send', 'slack_send', 'mcp-abc-send'])
+      )
+      expect(result.operations).toHaveLength(3)
+      expect(discoveredServerIds().sort()).toEqual([...serverIds].sort())
+    }
+  )
+
+  it.each([
+    ['mcp-deleted', 'MCP server not found'],
+    ['mcp-down', 'connect ECONNREFUSED'],
+    ['mcp-empty', 'No permitted MCP operations are available for mcp-empty'],
+  ])('fails a request that targets %s with its own error', async (serverId, message) => {
+    await expect(catalog({ service: `mcp:${serverId}` })).rejects.toThrow(message)
+    await expect(catalog({ toolId: `${serverId}-send` })).rejects.toThrow(message)
+  })
+})
@@ -7,6 +7,7 @@ import {
   resolvePrincipalSubjectUserId,
 } from '@sim/auth/principal'
 import { INTEGRATION_METADATA } from '@sim/deployment-config/integration-metadata'
+import { createLogger } from '@sim/logger'
 import { stripVersionSuffix } from '@sim/utils/string'
 import { defineWorkspaceOperation } from '@/lib/core/application'
 import { defineOrganizationOperation } from '@/lib/core/application/organization-operation'
@@ -33,6 +34,8 @@ import type {
 import { buildTaggedMcpToolSchemas } from '@/lib/mothership/mcp-tools'
 import { resolveActiveWorkspaceApplicationContext } from '@/lib/workspaces/application/context'
 
+const logger = createLogger('IntegrationCatalog')
+
 export const INTEGRATION_CATALOG_AUDIENCE = 'sim:integration-catalog'
 export const readIntegrationCatalogOperation = defineWorkspaceOperation({
   id: 'mothership.integrations.catalog',
@@ -227,12 +230,25 @@ const catalogUseCase = defineAuthorizedChatUseCase({
       const executorContext = input.mcpExecution
         ? catalogExecutorContext(input, context.userId, workspaceId)
         : undefined
-      const mcpTools = await buildTaggedMcpToolSchemas(
+      const { tools: mcpTools, failures } = await buildTaggedMcpToolSchemas(
         context.userId,
         workspaceId,
         candidates,
         executorContext
       )
+      const targetFailure = failures.find(
+        ({ serverId }) =>
+          input.service === `mcp:${serverId}` ||
+          (input.toolId?.startsWith(`${serverId}-`) &&
+            !mcpTools.some((tool) => tool.name === input.toolId))
+      )
+      if (targetFailure) throw targetFailure.error
+      for (const { serverId, error } of failures) {
+        logger.warn('Omitting an undiscoverable tagged MCP server from the integration catalog', {
+          serverId,
+          reason: error.message,
+        })
+      }
       tools.push(
         ...mcpTools.filter(
           (tool) => selectedIds.has(tool.name) || serverIds.has(tool.service?.slice(4) ?? '')