diff --git a/src/plugin-handlers/agent-config-handler.test.ts b/src/plugin-handlers/agent-config-handler.test.ts
new file mode 100644
index 000000000..c0d13016c
--- /dev/null
+++ b/src/plugin-handlers/agent-config-handler.test.ts
@@ -0,0 +1,197 @@
+/// <reference types="bun-types" />
+
+import type { AgentConfig } from "@opencode-ai/sdk"
+import { afterEach, beforeEach, describe, expect, spyOn, test } from "bun:test"
+import * as agents from "../agents"
+import * as shared from "../shared"
+import * as sisyphusJunior from "../agents/sisyphus-junior"
+import type { OhMyOpenCodeConfig } from "../config"
+import * as agentLoader from "../features/claude-code-agent-loader"
+import * as skillLoader from "../features/opencode-skill-loader"
+import { getAgentDisplayName } from "../shared/agent-display-names"
+import { applyAgentConfig } from "./agent-config-handler"
+import type { PluginComponents } from "./plugin-components-loader"
+
+const BUILTIN_SISYPHUS_DISPLAY_NAME = getAgentDisplayName("sisyphus")
+
+function createPluginComponents(): PluginComponents {
+  return {
+    commands: {},
+    skills: {},
+    agents: {},
+    mcpServers: {},
+    hooksConfigs: [],
+    plugins: [],
+    errors: [],
+  }
+}
+
+function createBaseConfig(): Record<string, unknown> {
+  return {
+    model: "anthropic/claude-opus-4-6",
+    agent: {},
+  }
+}
+
+function createPluginConfig(): OhMyOpenCodeConfig {
+  return {
+    sisyphus_agent: {
+      planner_enabled: false,
+    },
+  }
+}
+
+describe("applyAgentConfig builtin override protection", () => {
+  let createBuiltinAgentsSpy: ReturnType<typeof spyOn>
+  let createSisyphusJuniorAgentSpy: ReturnType<typeof spyOn>
+  let discoverConfigSourceSkillsSpy: ReturnType<typeof spyOn>
+  let discoverUserClaudeSkillsSpy: ReturnType<typeof spyOn>
+  let discoverProjectClaudeSkillsSpy: ReturnType<typeof spyOn>
+  let discoverOpencodeGlobalSkillsSpy: ReturnType<typeof spyOn>
+  let discoverOpencodeProjectSkillsSpy: ReturnType<typeof spyOn>
+  let loadUserAgentsSpy: ReturnType<typeof spyOn>
+  let loadProjectAgentsSpy: ReturnType<typeof spyOn>
+  let migrateAgentConfigSpy: ReturnType<typeof spyOn>
+  let logSpy: ReturnType<typeof spyOn>
+
+  const builtinSisyphusConfig: AgentConfig = {
+    name: "Builtin Sisyphus",
+    prompt: "builtin prompt",
+    mode: "primary",
+  }
+
+  const builtinOracleConfig: AgentConfig = {
+    name: "oracle",
+    prompt: "oracle prompt",
+    mode: "subagent",
+  }
+
+  const sisyphusJuniorConfig: AgentConfig = {
+    name: "Sisyphus-Junior",
+    prompt: "junior prompt",
+    mode: "all",
+  }
+
+  beforeEach(() => {
+    createBuiltinAgentsSpy = spyOn(agents, "createBuiltinAgents").mockResolvedValue({
+      sisyphus: builtinSisyphusConfig,
+      oracle: builtinOracleConfig,
+    })
+
+    createSisyphusJuniorAgentSpy = spyOn(
+      sisyphusJunior,
+      "createSisyphusJuniorAgentWithOverrides",
+    ).mockReturnValue(sisyphusJuniorConfig)
+
+    discoverConfigSourceSkillsSpy = spyOn(
+      skillLoader,
+      "discoverConfigSourceSkills",
+    ).mockResolvedValue([])
+    discoverUserClaudeSkillsSpy = spyOn(
+      skillLoader,
+      "discoverUserClaudeSkills",
+    ).mockResolvedValue([])
+    discoverProjectClaudeSkillsSpy = spyOn(
+      skillLoader,
+      "discoverProjectClaudeSkills",
+    ).mockResolvedValue([])
+    discoverOpencodeGlobalSkillsSpy = spyOn(
+      skillLoader,
+      "discoverOpencodeGlobalSkills",
+    ).mockResolvedValue([])
+    discoverOpencodeProjectSkillsSpy = spyOn(
+      skillLoader,
+      "discoverOpencodeProjectSkills",
+    ).mockResolvedValue([])
+
+    loadUserAgentsSpy = spyOn(agentLoader, "loadUserAgents").mockReturnValue({})
+    loadProjectAgentsSpy = spyOn(agentLoader, "loadProjectAgents").mockReturnValue({})
+
+    migrateAgentConfigSpy = spyOn(shared, "migrateAgentConfig").mockImplementation(
+      (config: Record<string, unknown>) => config,
+    )
+    logSpy = spyOn(shared, "log").mockImplementation(() => {})
+  })
+
+  afterEach(() => {
+    createBuiltinAgentsSpy.mockRestore()
+    createSisyphusJuniorAgentSpy.mockRestore()
+    discoverConfigSourceSkillsSpy.mockRestore()
+    discoverUserClaudeSkillsSpy.mockRestore()
+    discoverProjectClaudeSkillsSpy.mockRestore()
+    discoverOpencodeGlobalSkillsSpy.mockRestore()
+    discoverOpencodeProjectSkillsSpy.mockRestore()
+    loadUserAgentsSpy.mockRestore()
+    loadProjectAgentsSpy.mockRestore()
+    migrateAgentConfigSpy.mockRestore()
+    logSpy.mockRestore()
+  })
+
+  test("filters user agents whose key matches the builtin display-name alias", async () => {
+    // given
+    loadUserAgentsSpy.mockReturnValue({
+      [BUILTIN_SISYPHUS_DISPLAY_NAME]: {
+        name: BUILTIN_SISYPHUS_DISPLAY_NAME,
+        prompt: "user alias prompt",
+        mode: "subagent",
+      },
+    })
+
+    // when
+    const result = await applyAgentConfig({
+      config: createBaseConfig(),
+      pluginConfig: createPluginConfig(),
+      ctx: { directory: "/tmp" },
+      pluginComponents: createPluginComponents(),
+    })
+
+    // then
+    expect(result[BUILTIN_SISYPHUS_DISPLAY_NAME]).toEqual(builtinSisyphusConfig)
+  })
+
+  test("filters user agents whose key differs from a builtin key only by case", async () => {
+    // given
+    loadUserAgentsSpy.mockReturnValue({
+      SiSyPhUs: {
+        name: "SiSyPhUs",
+        prompt: "mixed-case prompt",
+        mode: "subagent",
+      },
+    })
+
+    // when
+    const result = await applyAgentConfig({
+      config: createBaseConfig(),
+      pluginConfig: createPluginConfig(),
+      ctx: { directory: "/tmp" },
+      pluginComponents: createPluginComponents(),
+    })
+
+    // then
+    expect(result[BUILTIN_SISYPHUS_DISPLAY_NAME]).toEqual(builtinSisyphusConfig)
+    expect(result.SiSyPhUs).toBeUndefined()
+  })
+
+  test("filters plugin agents whose key matches the builtin display-name alias", async () => {
+    // given
+    const pluginComponents = createPluginComponents()
+    pluginComponents.agents = {
+      [BUILTIN_SISYPHUS_DISPLAY_NAME]: {
+        name: BUILTIN_SISYPHUS_DISPLAY_NAME,
+        prompt: "plugin alias prompt",
+        mode: "subagent",
+      },
+    }
+
+    // when
+    const result = await applyAgentConfig({
+      config: createBaseConfig(),
+      pluginConfig: createPluginConfig(),
+      ctx: { directory: "/tmp" },
+      pluginComponents,
+    })
+
+    // then
+    expect(result[BUILTIN_SISYPHUS_DISPLAY_NAME]).toEqual(builtinSisyphusConfig)
+  })
+})
diff --git a/src/plugin-handlers/agent-config-handler.ts b/src/plugin-handlers/agent-config-handler.ts
index ac4c00bcc..4f5ad9eaf 100644
--- a/src/plugin-handlers/agent-config-handler.ts
+++ b/src/plugin-handlers/agent-config-handler.ts
@@ -15,6 +15,10 @@ import { loadProjectAgents, loadUserAgents } from "../features/claude-code-agent
 import type { PluginComponents } from "./plugin-components-loader";
 import { reorderAgentsByPriority } from "./agent-priority-order";
 import { remapAgentKeysToDisplayNames } from "./agent-key-remapper";
+import {
+  createProtectedAgentNameSet,
+  filterProtectedAgentOverrides,
+} from "./agent-override-protection";
 import { buildPrometheusAgentConfig } from "./prometheus-agent-config-builder";
 import { buildPlanDemoteConfig } from "./plan-model-inheritance";
 
@@ -209,19 +213,21 @@ export async function applyAgentConfig(params: {
         )
       : undefined;
 
-    // Collect all builtin agent names to prevent user/project .md files from overriding them
-    const builtinAgentNames = new Set([
+    const protectedBuiltinAgentNames = createProtectedAgentNameSet([
       ...Object.keys(agentConfig),
       ...Object.keys(builtinAgents),
     ]);
-
-    // Filter user/project agents that duplicate builtin agents (they have mode: "subagent" hardcoded
-    // in loadAgentsFromDir which would incorrectly override the builtin mode: "primary")
-    const filteredUserAgents = Object.fromEntries(
-      Object.entries(userAgents).filter(([key]) => !builtinAgentNames.has(key)),
+    const filteredUserAgents = filterProtectedAgentOverrides(
+      userAgents,
+      protectedBuiltinAgentNames,
     );
-    const filteredProjectAgents = Object.fromEntries(
-      Object.entries(projectAgents).filter(([key]) => !builtinAgentNames.has(key)),
+    const filteredProjectAgents = filterProtectedAgentOverrides(
+      projectAgents,
+      protectedBuiltinAgentNames,
+    );
+    const filteredPluginAgents = filterProtectedAgentOverrides(
+      pluginAgents,
+      protectedBuiltinAgentNames,
     );
 
     params.config.agent = {
@@ -231,26 +237,33 @@ export async function applyAgentConfig(params: {
       ),
       ...filterDisabledAgents(filteredUserAgents),
       ...filterDisabledAgents(filteredProjectAgents),
-      ...filterDisabledAgents(pluginAgents),
+      ...filterDisabledAgents(filteredPluginAgents),
       ...filteredConfigAgents,
       build: { ...migratedBuild, mode: "subagent", hidden: true },
       ...(planDemoteConfig ? { plan: planDemoteConfig } : {}),
     };
   } else {
-    // Filter user/project agents that duplicate builtin agents
-    const builtinAgentNames = new Set(Object.keys(builtinAgents));
-    const filteredUserAgents = Object.fromEntries(
-      Object.entries(userAgents).filter(([key]) => !builtinAgentNames.has(key)),
+    const protectedBuiltinAgentNames = createProtectedAgentNameSet(
+      Object.keys(builtinAgents),
     );
-    const filteredProjectAgents = Object.fromEntries(
-      Object.entries(projectAgents).filter(([key]) => !builtinAgentNames.has(key)),
+    const filteredUserAgents = filterProtectedAgentOverrides(
+      userAgents,
+      protectedBuiltinAgentNames,
+    );
+    const filteredProjectAgents = filterProtectedAgentOverrides(
+      projectAgents,
+      protectedBuiltinAgentNames,
+    );
+    const filteredPluginAgents = filterProtectedAgentOverrides(
+      pluginAgents,
+      protectedBuiltinAgentNames,
     );
 
     params.config.agent = {
       ...builtinAgents,
       ...filterDisabledAgents(filteredUserAgents),
       ...filterDisabledAgents(filteredProjectAgents),
-      ...filterDisabledAgents(pluginAgents),
+      ...filterDisabledAgents(filteredPluginAgents),
       ...configAgent,
     };
   }
diff --git a/src/plugin-handlers/agent-override-protection.ts b/src/plugin-handlers/agent-override-protection.ts
new file mode 100644
index 000000000..389a54af9
--- /dev/null
+++ b/src/plugin-handlers/agent-override-protection.ts
@@ -0,0 +1,29 @@
+const PARENTHETICAL_SUFFIX_PATTERN = /\s*(\([^)]*\)\s*)+$/u
+
+export function normalizeProtectedAgentName(agentName: string): string {
+  return agentName.trim().toLowerCase().replace(PARENTHETICAL_SUFFIX_PATTERN, "").trim()
+}
+
+export function createProtectedAgentNameSet(agentNames: Iterable<string>): Set<string> {
+  const protectedAgentNames = new Set<string>()
+
+  for (const agentName of agentNames) {
+    const normalizedAgentName = normalizeProtectedAgentName(agentName)
+    if (normalizedAgentName.length === 0) continue
+
+    protectedAgentNames.add(normalizedAgentName)
+  }
+
+  return protectedAgentNames
+}
+
+export function filterProtectedAgentOverrides<TAgent>(
+  agents: Record<string, TAgent>,
+  protectedAgentNames: ReadonlySet<string>,
+): Record<string, TAgent> {
+  return Object.fromEntries(
+    Object.entries(agents).filter(([agentName]) => {
+      return !protectedAgentNames.has(normalizeProtectedAgentName(agentName))
+    }),
+  )
+}