diff --git a/src/features/builtin-commands/commands.test.ts b/src/features/builtin-commands/commands.test.ts
index 15231bb44..8db604198 100644
--- a/src/features/builtin-commands/commands.test.ts
+++ b/src/features/builtin-commands/commands.test.ts
@@ -1,8 +1,17 @@
-import { describe, test, expect } from "bun:test"
+import { afterEach, beforeEach, describe, test, expect } from "bun:test"
 import { loadBuiltinCommands } from "./commands"
 import { HANDOFF_TEMPLATE } from "./templates/handoff"
 import { REMOVE_AI_SLOPS_TEMPLATE } from "./templates/remove-ai-slops"
 import type { BuiltinCommandName } from "./types"
+import { _resetForTesting, registerAgentName } from "../claude-code-session-state"
+
+beforeEach(() => {
+  _resetForTesting()
+})
+
+afterEach(() => {
+  _resetForTesting()
+})
 
 describe("loadBuiltinCommands", () => {
   test("should include handoff command in loaded commands", () => {
@@ -69,6 +78,17 @@ describe("loadBuiltinCommands", () => {
     //#then
     expect(commands["start-work"].agent).toBe("sisyphus")
   })
+
+  test("should preassign Atlas as the native agent for start-work when Atlas is registered", () => {
+    //#given
+    registerAgentName("atlas")
+
+    //#when
+    const commands = loadBuiltinCommands()
+
+    //#then
+    expect(commands["start-work"].agent).toBe("atlas")
+  })
 })
 
 describe("loadBuiltinCommands — remove-ai-slops", () => {
diff --git a/src/features/builtin-commands/commands.ts b/src/features/builtin-commands/commands.ts
index 3c0f1e432..8b82bd3a1 100644
--- a/src/features/builtin-commands/commands.ts
+++ b/src/features/builtin-commands/commands.ts
@@ -1,4 +1,5 @@
 import type { CommandDefinition } from "../claude-code-command-loader"
+import { isAgentRegistered } from "../claude-code-session-state"
 import type { BuiltinCommandName, BuiltinCommands } from "./types"
 import { INIT_DEEP_TEMPLATE } from "./templates/init-deep"
 import { RALPH_LOOP_TEMPLATE, ULW_LOOP_TEMPLATE, CANCEL_RALPH_TEMPLATE } from "./templates/ralph-loop"
@@ -8,58 +9,59 @@ import { START_WORK_TEMPLATE } from "./templates/start-work"
 import { HANDOFF_TEMPLATE } from "./templates/handoff"
 import { REMOVE_AI_SLOPS_TEMPLATE } from "./templates/remove-ai-slops"
 
-const BUILTIN_COMMAND_DEFINITIONS: Record<BuiltinCommandName, Omit<CommandDefinition, "name">> = {
-  "init-deep": {
-    description: "(builtin) Initialize hierarchical AGENTS.md knowledge base",
-    template: `<command-instruction>
+function createBuiltinCommandDefinitions(): Record<BuiltinCommandName, Omit<CommandDefinition, "name">> {
+  return {
+    "init-deep": {
+      description: "(builtin) Initialize hierarchical AGENTS.md knowledge base",
+      template: `<command-instruction>
 ${INIT_DEEP_TEMPLATE}
 </command-instruction>
 
 <user-request>
 $ARGUMENTS
 </user-request>`,
-    argumentHint: "[--create-new] [--max-depth=N]",
-  },
-   "ralph-loop": {
-     description: "(builtin) Start self-referential development loop until completion",
-     template: `<command-instruction>
+      argumentHint: "[--create-new] [--max-depth=N]",
+    },
+     "ralph-loop": {
+       description: "(builtin) Start self-referential development loop until completion",
+       template: `<command-instruction>
 ${RALPH_LOOP_TEMPLATE}
 </command-instruction>
 
 <user-task>
 $ARGUMENTS
 </user-task>`,
-     argumentHint: '"task description" [--completion-promise=TEXT] [--max-iterations=N] [--strategy=reset|continue]',
-   },
-   "ulw-loop": {
-      description: "(builtin) Start ultrawork loop - continues until completion with ultrawork mode",
-      template: `<command-instruction>
+       argumentHint: '"task description" [--completion-promise=TEXT] [--max-iterations=N] [--strategy=reset|continue]',
+     },
+     "ulw-loop": {
+        description: "(builtin) Start ultrawork loop - continues until completion with ultrawork mode",
+        template: `<command-instruction>
 ${ULW_LOOP_TEMPLATE}
 </command-instruction>
 
 <user-task>
 $ARGUMENTS
 </user-task>`,
-      argumentHint: '"task description" [--completion-promise=TEXT] [--strategy=reset|continue]',
-    },
-  "cancel-ralph": {
-    description: "(builtin) Cancel active Ralph Loop",
-    template: `<command-instruction>
+        argumentHint: '"task description" [--completion-promise=TEXT] [--strategy=reset|continue]',
+      },
+    "cancel-ralph": {
+      description: "(builtin) Cancel active Ralph Loop",
+      template: `<command-instruction>
 ${CANCEL_RALPH_TEMPLATE}
 </command-instruction>`,
-  },
-  refactor: {
-    description:
-      "(builtin) Intelligent refactoring command with LSP, AST-grep, architecture analysis, codemap, and TDD verification.",
-    template: `<command-instruction>
+    },
+    refactor: {
+      description:
+        "(builtin) Intelligent refactoring command with LSP, AST-grep, architecture analysis, codemap, and TDD verification.",
+      template: `<command-instruction>
 ${REFACTOR_TEMPLATE}
 </command-instruction>`,
-    argumentHint: "<refactoring-target> [--scope=<file|module|project>] [--strategy=<safe|aggressive>]",
-  },
-  "start-work": {
-    description: "(builtin) Start Sisyphus work session from Prometheus plan",
-    agent: "sisyphus",
-    template: `<command-instruction>
+      argumentHint: "<refactoring-target> [--scope=<file|module|project>] [--strategy=<safe|aggressive>]",
+    },
+    "start-work": {
+      description: "(builtin) Start Sisyphus work session from Prometheus plan",
+      agent: isAgentRegistered("atlas") ? "atlas" : "sisyphus",
+      template: `<command-instruction>
 ${START_WORK_TEMPLATE}
 </command-instruction>
 
@@ -71,27 +73,27 @@ Timestamp: $TIMESTAMP
 <user-request>
 $ARGUMENTS
 </user-request>`,
-    argumentHint: "[plan-name]",
-  },
-  "stop-continuation": {
-    description: "(builtin) Stop all continuation mechanisms (ralph loop, todo continuation, boulder) for this session",
-    template: `<command-instruction>
+      argumentHint: "[plan-name]",
+    },
+    "stop-continuation": {
+      description: "(builtin) Stop all continuation mechanisms (ralph loop, todo continuation, boulder) for this session",
+      template: `<command-instruction>
 ${STOP_CONTINUATION_TEMPLATE}
 </command-instruction>`,
-  },
-  "remove-ai-slops": {
-    description: "(builtin) Remove AI-generated code smells from branch changes and critically review the results",
-    template: `<command-instruction>
+    },
+    "remove-ai-slops": {
+      description: "(builtin) Remove AI-generated code smells from branch changes and critically review the results",
+      template: `<command-instruction>
 ${REMOVE_AI_SLOPS_TEMPLATE}
 </command-instruction>
 
 <user-request>
 $ARGUMENTS
 </user-request>`,
-  },
-  handoff: {
-    description: "(builtin) Create a detailed context summary for continuing work in a new session",
-    template: `<command-instruction>
+    },
+    handoff: {
+      description: "(builtin) Create a detailed context summary for continuing work in a new session",
+      template: `<command-instruction>
 ${HANDOFF_TEMPLATE}
 </command-instruction>
 
@@ -103,17 +105,19 @@ Timestamp: $TIMESTAMP
 <user-request>
 $ARGUMENTS
 </user-request>`,
-    argumentHint: "[goal]",
-  },
+      argumentHint: "[goal]",
+    },
+  }
 }
 
 export function loadBuiltinCommands(
   disabledCommands?: BuiltinCommandName[]
 ): BuiltinCommands {
+  const builtinCommandDefinitions = createBuiltinCommandDefinitions()
   const disabled = new Set(disabledCommands ?? [])
   const commands: BuiltinCommands = {}
 
-  for (const [name, definition] of Object.entries(BUILTIN_COMMAND_DEFINITIONS)) {
+  for (const [name, definition] of Object.entries(builtinCommandDefinitions)) {
     if (!disabled.has(name as BuiltinCommandName)) {
       const { argumentHint: _argumentHint, ...openCodeCompatible } = definition
       commands[name] = { ...openCodeCompatible, name } as CommandDefinition