diff --git a/docs/installation.md b/docs/installation.md
index 06a7a9d00..3d074e50c 100644
--- a/docs/installation.md
+++ b/docs/installation.md
@@ -51,20 +51,24 @@ mechanics:
 - use the bundled skill for a repeatable investigation workflow.
 
 REA then summarizes the detected clients and asks which capabilities to set up.
-The capability picker starts empty and presents `Agent integration` (the MCP
-registration and matching guided workflow together) plus the optional Hopper
-provider. Selecting agent integration opens a second empty checklist for the
-exact detected agents that should receive a registration. Detection provides
-context; it does not preselect or authorize a configuration write.
+The capability picker pre-selects `Agent integration` (the MCP registration and
+matching guided workflow together) when detected agents exist, and presents the
+optional Hopper provider alongside it. Selecting agent integration opens a second
+checklist for the exact detected agents that should receive a registration; all
+detected agents are pre-selected. Detection provides context and pre-selection;
+it does not authorize a configuration write until the user confirms.
 
-Choosing no capabilities exits without changes. Selecting the provider does not
-implicitly select an agent, and selecting agent integration does not include
-every detected agent. The picker keeps its navigation, selection, confirmation,
-and cancellation keys visible instead of relying on a transient hint.
+Because the user has explicitly invoked `rea setup`, the wizard biases toward the
+happy path: capabilities and agents are pre-selected, and the final approval
+defaults to **Yes**. The user can still deselect any item or cancel at any prompt.
+Choosing no capabilities exits without changes. Selecting agent integration
+always includes the bundled skill, even if all agents are deselected. The picker
+keeps its navigation, selection, confirmation, and cancellation keys visible
+instead of relying on a transient hint.
 
 Every selected path converges on the same exact preflight. REA validates the
 current state, prints the proposed effects, and asks for final approval with
-**No** as the default. Selection alone never authorizes a mutation. The plan
+**Yes** as the default. Selection alone never authorizes a mutation. The plan
 identifies:
 
 - an existing Hopper installation, a validated bring-your-own Ghidra environment, or the official Hopper package it proposes to install;
diff --git a/src/cliSetup.ts b/src/cliSetup.ts
index 69b925643..0cd3ea434 100644
--- a/src/cliSetup.ts
+++ b/src/cliSetup.ts
@@ -61,7 +61,7 @@ export const confirmInteractiveSetup = async (
       selectedActions.length === 1
         ? "Apply this change?"
         : `Apply these ${String(selectedActions.length)} changes?`,
-    initialValue: false,
+    initialValue: true,
     active: "Yes, apply",
     inactive: "No, cancel",
   });
@@ -131,9 +131,10 @@ const selectSetupActions = async (
     ({ kind }) => kind !== "configure_client",
   );
   const capabilities = setupCapabilities(clientActions, componentActions);
+  const preselectedCapabilityIds = defaultCapabilityIds(capabilities);
   const selectedCapabilities = accessible
-    ? await selectCapabilitiesAccessibly(capabilities)
-    : await selectCapabilities(capabilities);
+    ? await selectCapabilitiesAccessibly(capabilities, preselectedCapabilityIds)
+    : await selectCapabilities(capabilities, preselectedCapabilityIds);
   if (selectedCapabilities === undefined) return undefined;
   const selectedCapabilityIds = new Set(selectedCapabilities);
   const bundledSkillAction = componentActions.find(
@@ -147,23 +148,35 @@ const selectSetupActions = async (
     .map(({ id }) => id);
   if (!selectedCapabilityIds.has(agentIntegrationCapabilityId))
     return selectedActionIds;
+  const bundledSkillId =
+    bundledSkillAction === undefined ? undefined : bundledSkillAction.id;
   if (clientActions.length === 0)
     return [
-      ...(bundledSkillAction === undefined ? [] : [bundledSkillAction.id]),
+      ...(bundledSkillId === undefined ? [] : [bundledSkillId]),
       ...selectedActionIds,
     ];
+  const preselectedClientIds = clientActions.map(({ id }) => id);
   const selectedClients = accessible
-    ? await selectClientsAccessibly(clientActions)
-    : await selectClients(clientActions);
+    ? await selectClientsAccessibly(clientActions, preselectedClientIds)
+    : await selectClients(clientActions, preselectedClientIds);
   if (selectedClients === undefined) return undefined;
-  if (selectedClients.length === 0) return selectedActionIds;
   return [
     ...selectedClients,
-    ...(bundledSkillAction === undefined ? [] : [bundledSkillAction.id]),
+    ...(bundledSkillId === undefined ? [] : [bundledSkillId]),
     ...selectedActionIds,
   ];
 };
 
+const defaultCapabilityIds = (
+  capabilities: readonly SetupCapability[],
+): readonly string[] => {
+  const hasAgentIntegration = capabilities.some(
+    ({ id }) => id === agentIntegrationCapabilityId,
+  );
+  if (!hasAgentIntegration) return [];
+  return [agentIntegrationCapabilityId];
+};
+
 const setupCapabilities = (
   clientActions: readonly SetupAction[],
   componentActions: readonly SetupAction[],
@@ -192,6 +205,7 @@ const setupCapabilities = (
 
 const selectCapabilities = async (
   capabilities: readonly SetupCapability[],
+  initialValues: readonly string[],
 ): Promise<readonly string[] | undefined> => {
   const selection = await multiselect({
     ...promptStreams,
@@ -201,6 +215,7 @@ const selectCapabilities = async (
       label: capability.label,
       hint: capability.hint,
     })),
+    initialValues: [...initialValues],
     required: false,
     maxItems: Math.max(
       3,
@@ -213,13 +228,15 @@ const selectCapabilities = async (
 
 const selectCapabilitiesAccessibly = async (
   capabilities: readonly SetupCapability[],
+  preselectedIds: readonly string[],
 ): Promise<readonly string[] | undefined> => {
+  const preselected = new Set(preselectedIds);
   const selected: string[] = [];
   for (const capability of capabilities) {
     const included = await confirm({
       ...promptStreams,
       message: `Set up ${capability.label}? ${capability.hint}`,
-      initialValue: false,
+      initialValue: preselected.has(capability.id),
       vertical: true,
     });
     if (isCancel(included)) return undefined;
@@ -230,6 +247,7 @@ const selectCapabilitiesAccessibly = async (
 
 const selectClients = async (
   actions: readonly SetupAction[],
+  initialValues: readonly string[],
 ): Promise<readonly string[] | undefined> => {
   const selection = await multiselect({
     ...promptStreams,
@@ -237,8 +255,9 @@ const selectClients = async (
     options: actions.map((action) => ({
       value: action.id,
       label: `${action.label} (detected)`,
-      hint: `${action.operation} · ${action.target}`,
+      hint: `Configure the REA MCP server for ${action.label}`,
     })),
+    initialValues: [...initialValues],
     required: false,
     maxItems: Math.max(
       3,
@@ -251,13 +270,15 @@ const selectClients = async (
 
 const selectClientsAccessibly = async (
   actions: readonly SetupAction[],
+  initialValues: readonly string[],
 ): Promise<readonly string[] | undefined> => {
+  const preselected = new Set(initialValues);
   const selected: string[] = [];
   for (const action of actions) {
     const included = await confirm({
       ...promptStreams,
       message: `Configure ${action.label}? ${action.target}`,
-      initialValue: false,
+      initialValue: preselected.has(action.id),
       vertical: true,
     });
     if (isCancel(included)) return undefined;
diff --git a/tests/cliSetup.test.ts b/tests/cliSetup.test.ts
index fbc58a332..5928acce4 100644
--- a/tests/cliSetup.test.ts
+++ b/tests/cliSetup.test.ts
@@ -64,8 +64,8 @@ describe("interactive setup journey", () => {
     expect(result.decision.approved).toBe(false);
   });
 
-  it("does not turn available capabilities into selected setup actions", async () => {
-    const result = await runJourney([step("What should REA set up?", "\r")]);
+  it("allows deselecting the pre-selected agent integration to opt out", async () => {
+    const result = await runJourney([step("What should REA set up?", " \r")]);
 
     expect(result.output).toContain(
       "Agent integration (MCP + guided workflow)",
@@ -82,9 +82,20 @@ describe("interactive setup journey", () => {
     });
   });
 
+  it("pre-selects agent integration and proceeds to the agent picker on Enter", async () => {
+    const result = await runJourney([
+      step("What should REA set up?", "\r"),
+      step("Which agents should use REA?", "\u0003"),
+    ]);
+
+    expect(result.output).toContain("Codex (detected)");
+    expect(result.output).toContain("Setup cancelled. No changes were made.");
+    expect(result.decision.approved).toBe(false);
+  });
+
   it("offers one bundled repair when MCP is aligned but the skill is missing", async () => {
     const result = await runJourney(
-      [step("What should REA set up?", "\r")],
+      [step("What should REA set up?", "\r"), step("Apply this change?", "\r")],
       false,
       actions.filter(({ kind }) => kind !== "configure_client"),
     );
@@ -96,13 +107,16 @@ describe("interactive setup journey", () => {
     expect(result.output).not.toContain(
       "REA reverse-engineering skill (skill)",
     );
-    expect(result.decision.selectedActionIds).toEqual([]);
+    expect(result.decision).toEqual({
+      approved: true,
+      selectedActionIds: ["install_skill"],
+    });
   });
 
-  it("shows multiple detected agents without preselecting either one", async () => {
+  it("pre-selects all detected agents in the agent picker", async () => {
     const result = await runJourney(
       [
-        step("What should REA set up?", " \r"),
+        step("What should REA set up?", "\r"),
         step("Which agents should use REA?", "\u0003"),
       ],
       false,
@@ -123,21 +137,26 @@ describe("interactive setup journey", () => {
     expect(result.decision.approved).toBe(false);
   });
 
-  it("asks for agent targets only after agent integration is selected", async () => {
+  it("retains the bundled skill even when all agents are deselected (#399)", async () => {
     const result = await runJourney([
-      step("What should REA set up?", " \r"),
-      step("Which agents should use REA?", "\u0003"),
+      step("What should REA set up?", "\r"),
+      step("Which agents should use REA?", " \r"),
+      step("Apply this change?", "\r"),
     ]);
 
-    expect(result.output).toContain("Codex (detected)");
-    expect(result.output).toContain("Setup cancelled. No changes were made.");
-    expect(result.decision.approved).toBe(false);
+    expect(result.output).toContain("Ready to review");
+    expect(result.output).toContain("INSTALL  REA reverse-engineering skill");
+    expect(result.output).not.toContain("CREATE  Codex");
+    expect(result.decision).toEqual({
+      approved: true,
+      selectedActionIds: ["install_skill"],
+    });
   });
 
-  it("reviews only explicitly selected actions with default-No consent", async () => {
+  it("defaults the final confirmation to Yes, apply", async () => {
     const result = await runJourney([
-      step("What should REA set up?", " \r"),
-      step("Which agents should use REA?", " \r"),
+      step("What should REA set up?", "\r"),
+      step("Which agents should use REA?", "\r"),
       step("Apply these 2 changes?", "\r"),
     ]);
 
@@ -148,7 +167,21 @@ describe("interactive setup journey", () => {
     expect(result.output).not.toContain(
       "INSTALL  Hopper deep-analysis provider",
     );
-    expect(result.output).toContain("No, cancel");
+    expect(result.output).toContain("Yes, apply");
+    expect(result.decision).toEqual({
+      approved: true,
+      selectedActionIds: ["configure_client:codex", "install_skill"],
+    });
+  });
+
+  it("can still be cancelled at the final confirmation", async () => {
+    const result = await runJourney([
+      step("What should REA set up?", "\r"),
+      step("Which agents should use REA?", "\r"),
+      step("Apply these 2 changes?", "\u001b[D\r"),
+    ]);
+
+    expect(result.output).toContain("Ready to review");
     expect(result.output).toContain("Setup cancelled. No changes were made.");
     expect(result.decision).toEqual({
       approved: false,
@@ -158,10 +191,7 @@ describe("interactive setup journey", () => {
 
   it("repairs an aligned agent integration through the bundled option", async () => {
     const result = await runJourney(
-      [
-        step("What should REA set up?", " \r"),
-        step("Apply this change?", "\r"),
-      ],
+      [step("What should REA set up?", "\r"), step("Apply this change?", "\r")],
       false,
       actions.filter(({ kind }) => kind !== "configure_client"),
     );
@@ -175,21 +205,40 @@ describe("interactive setup journey", () => {
       "INSTALL  Hopper deep-analysis provider",
     );
     expect(result.decision).toEqual({
-      approved: false,
+      approved: true,
       selectedActionIds: ["install_skill"],
     });
   });
 
-  it("keeps every accessible capability prompt defaulted to skip", async () => {
+  it("defaults accessible agent integration to Yes and others to No", async () => {
     const result = await runJourney(
       [
         step("Set up Agent integration (MCP + guided workflow)?", "\r"),
         step("Set up Hopper deep-analysis provider (provider)?", "\r"),
+        step("Apply this change?", "\r"),
+      ],
+      true,
+      actions.filter(({ kind }) => kind !== "configure_client"),
+    );
+
+    expect(result.output).toContain("Ready to review");
+    expect(result.output).toContain("INSTALL  REA reverse-engineering skill");
+    expect(result.decision).toEqual({
+      approved: true,
+      selectedActionIds: ["install_skill"],
+    });
+  });
+
+  it("allows accessible opt-out of the pre-selected agent integration", async () => {
+    const result = await runJourney(
+      [
+        step("Set up Agent integration (MCP + guided workflow)?", "\u001b[B\r"),
+        step("Set up Hopper deep-analysis provider (provider)?", "\r"),
       ],
       true,
     );
 
-    expect(result.output).not.toContain("Ready to review");
+    expect(result.output).toContain("Nothing selected. No changes were made.");
     expect(result.decision.selectedActionIds).toEqual([]);
   });