diff --git a/packages/mosaic/framework/fleet/README.md b/packages/mosaic/framework/fleet/README.md
index df42327f..b56c8451 100644
--- a/packages/mosaic/framework/fleet/README.md
+++ b/packages/mosaic/framework/fleet/README.md
@@ -12,6 +12,33 @@ The default tmux socket is `mosaic-fleet` so fleet commands do not touch the
 default tmux server. The roster is the desired-state authority; generated environment files are
 rebuildable projections, never a second source of configuration.
 
+## Brain-home split (fleet state vs framework templates)
+
+When a mosaic-brain clone is present, fleet **state** resolves from the brain
+home while framework templates and dispatch state stay in the config home
+(three-tree model, canon `docs/STRUCTURE-CANON.md` §2):
+
+| Path                                                                            | Without brain (legacy)                | With brain                     |
+| ------------------------------------------------------------------------------- | ------------------------------------- | ------------------------------ |
+| `fleet/agents/<seat>.env.*`                                                     | `~/.config/mosaic/fleet/agents/`      | `~/.mosaic/fleet/agents/`      |
+| `fleet/roles.local/` (overrides)                                                | `~/.config/mosaic/fleet/roles.local/` | `~/.mosaic/fleet/roles.local/` |
+| `fleet/profiles/` (working copies)                                              | `~/.config/mosaic/fleet/profiles/`    | `~/.mosaic/fleet/profiles/`    |
+| `fleet/roster.yaml`, `fleet/roles/` (baseline), `fleet/run/`, `fleet/services/` | `~/.config/mosaic/fleet/…`            | unchanged (config home)        |
+
+Activation (`packages/mosaic/src/fleet/brain-home.ts`, mirrored in
+`tools/fleet/start-agent-session.sh`):
+
+1. `MOSAIC_BRAIN_HOME` env var — explicit, always wins.
+2. Canonical `~/.mosaic` — adopted only when `MOSAIC_HOME` is the default
+   `~/.config/mosaic` AND `~/.mosaic/fleet/agents` exists. Custom
+   `--mosaic-home` values (tests, sandboxes, canaries) never adopt, keeping
+   them hermetic.
+3. Otherwise the config home (legacy single-tree behavior).
+
+Seat env dirs under a brain are subject to the same privacy boundary (0700
+dirs, 0600 files); `.env.generated` files are structure-valuable and tracked
+in the brain repo, hand-maintained `.env`/`.env.local` stay ignored and private.
+
 ## Examples
 
 - `examples/minimal.yaml` starts one local canary slot.
diff --git a/packages/mosaic/framework/tools/fleet/start-agent-session.sh b/packages/mosaic/framework/tools/fleet/start-agent-session.sh
index 6faffa38..f07470be 100755
--- a/packages/mosaic/framework/tools/fleet/start-agent-session.sh
+++ b/packages/mosaic/framework/tools/fleet/start-agent-session.sh
@@ -80,6 +80,26 @@ safe_path "$MOSAIC_HOME" || fail_env unsafe-path MOSAIC_HOME "$MOSAIC_HOME"
 
 FLEET_DIR="$MOSAIC_HOME/fleet"
 AGENT_ENV_DIR="$FLEET_DIR/agents"
+
+# Brain-home split (canon docs/STRUCTURE-CANON.md §2): seat launch envs live
+# under the brain home's fleet/agents when a brain is active; roster, roles
+# baseline, and runtime state (fleet/run) stay under MOSAIC_HOME.
+# Resolution mirrors packages/mosaic/src/fleet/brain-home.ts:
+#   1. MOSAIC_BRAIN_HOME env (explicit, always wins)
+#   2. ~/.mosaic — adopted only when MOSAIC_HOME is the default config home AND
+#      ~/.mosaic/fleet/agents exists
+#   3. MOSAIC_HOME (legacy single-tree)
+BRAIN_HOME="${MOSAIC_BRAIN_HOME:-}"
+if [ -z "$BRAIN_HOME" ]; then
+  BRAIN_HOME="$MOSAIC_HOME"
+  if [ "$(cd "$MOSAIC_HOME" 2>/dev/null && pwd -P)" = "$HOME/.config/mosaic" ] \
+     && [ -d "$HOME/.mosaic/fleet/agents" ]; then
+    BRAIN_HOME="$HOME/.mosaic"
+  fi
+fi
+if [ "$BRAIN_HOME" != "$MOSAIC_HOME" ]; then
+  AGENT_ENV_DIR="$BRAIN_HOME/fleet/agents"
+fi
 assert_managed_directory "$MOSAIC_HOME"
 assert_managed_directory "$FLEET_DIR"
 assert_private_directory "$AGENT_ENV_DIR"
diff --git a/packages/mosaic/framework/tools/fleet/test-start-agent-session.sh b/packages/mosaic/framework/tools/fleet/test-start-agent-session.sh
index e7d8e94f..1f84e2da 100755
--- a/packages/mosaic/framework/tools/fleet/test-start-agent-session.sh
+++ b/packages/mosaic/framework/tools/fleet/test-start-agent-session.sh
@@ -167,6 +167,54 @@ if echo "$valid_args" | grep -qF 'bash -c'; then
   fail "launcher constructed a shell command payload"
 fi
 
+# ── Brain-home split (canon §2) ─────────────────────────────────────────
+# When MOSAIC_HOME is the default config home under $HOME and the host carries
+# $HOME/.mosaic/fleet/agents, seat envs resolve from the brain tree; the config
+# home still owns fleet/run (holder-owner) and remains a managed boundary.
+: > "$TMUX_CALLS"
+HOME_BRAIN="$ROOT/brain-home"
+CONFIG_HOME="$HOME_BRAIN/.config/mosaic"
+BRAIN="$HOME_BRAIN/.mosaic"
+mkdir -p "$CONFIG_HOME/fleet/run" "$BRAIN/fleet/agents" "$HOME_BRAIN/work"
+chmod 700 "$CONFIG_HOME" "$CONFIG_HOME/fleet" "$CONFIG_HOME/fleet/run" \
+  "$BRAIN/fleet/agents" "$HOME_BRAIN/work"
+printf '123e4567-e89b-12d3-a456-426614174000\n' > "$CONFIG_HOME/fleet/run/holder-owner"
+chmod 600 "$CONFIG_HOME/fleet/run/holder-owner"
+cat > "$BRAIN/fleet/agents/coder-brain.env.generated" <<EOF
+MOSAIC_AGENT_NAME=coder-brain
+MOSAIC_AGENT_CLASS=code
+MOSAIC_AGENT_RUNTIME=pi
+MOSAIC_AGENT_MODEL=openai-codex/gpt-5.6-sol
+MOSAIC_AGENT_REASONING=high
+MOSAIC_AGENT_TOOL_POLICY=code
+MOSAIC_AGENT_WORKDIR=$HOME_BRAIN/work
+MOSAIC_TMUX_SOCKET=mosaic-test
+EOF
+chmod 600 "$BRAIN/fleet/agents/coder-brain.env.generated"
+install_pane_binaries "$HOME_BRAIN"
+HOME="$HOME_BRAIN" PATH="$FAKE_BIN:$PATH" MOSAIC_TEST_TMUX_CALLS="$TMUX_CALLS" \
+  MOSAIC_TEST_PANE_PID=$$ MOSAIC_TEST_HOME="$HOME_BRAIN" \
+  MOSAIC_TEST_FLEET_OWNER=123e4567-e89b-12d3-a456-426614174000 \
+  MOSAIC_HOME="$CONFIG_HOME" "$START" coder-brain
+brain_args=$(tr '\0' '\n' < "$TMUX_CALLS")
+echo "$brain_args" | grep -qF new-session || fail "brain-home generated projection did not reach tmux"
+echo "$brain_args" | grep -qF 'coder-brain' || fail "brain-home agent env was not the launch source"
+[ -f "$BRAIN/fleet/agents/coder-brain.env.generated" ] || fail "brain generated env vanished"
+
+# Negative control: the SAME default-config-home shape but without
+# ~/.mosaic/fleet/agents — the config-home env tree is used directly (legacy).
+: > "$TMUX_CALLS"
+HOME_NOBRAIN="$ROOT/brainless-home"
+CONFIG_HOME_NOBRAIN="$HOME_NOBRAIN/.config/mosaic"
+write_generated "$CONFIG_HOME_NOBRAIN" "coder-legacy"
+install_pane_binaries "$HOME_NOBRAIN"
+HOME="$HOME_NOBRAIN" PATH="$FAKE_BIN:$PATH" MOSAIC_TEST_TMUX_CALLS="$TMUX_CALLS" \
+  MOSAIC_TEST_PANE_PID=$$ MOSAIC_TEST_HOME="$HOME_NOBRAIN" \
+  MOSAIC_TEST_FLEET_OWNER=123e4567-e89b-12d3-a456-426614174000 \
+  MOSAIC_HOME="$CONFIG_HOME_NOBRAIN" "$START" coder-legacy
+legacy_args=$(tr '\0' '\n' < "$TMUX_CALLS")
+echo "$legacy_args" | grep -qF new-session || fail "legacy single-tree launch regressed"
+
 # The pane must start through an absolute clean-environment boundary. Its
 # runtime command remains an argv vector, but no holder/session environment
 # control variable can pass through the pane command.
diff --git a/packages/mosaic/src/commands/fleet-agent-crud-command.ts b/packages/mosaic/src/commands/fleet-agent-crud-command.ts
index b2aac15d..8085f708 100644
--- a/packages/mosaic/src/commands/fleet-agent-crud-command.ts
+++ b/packages/mosaic/src/commands/fleet-agent-crud-command.ts
@@ -1,5 +1,6 @@
 import { readFile } from 'node:fs/promises';
 import { join, resolve } from 'node:path';
+import { fleetAgentEnvDir, fleetRolesLocalDir } from '../fleet/brain-home.js';
 import type { Command } from 'commander';
 import {
   executeFleetAgentMutation,
@@ -149,9 +150,9 @@ async function executeCommand(
     request,
     mosaicHome,
     rosterPath,
-    agentEnvDir: join(mosaicHome, 'fleet', 'agents'),
+    agentEnvDir: fleetAgentEnvDir(mosaicHome),
     rolesDir: join(mosaicHome, 'fleet', 'roles'),
-    overrideDir: join(mosaicHome, 'fleet', 'roles.local'),
+    overrideDir: fleetRolesLocalDir(mosaicHome),
     dryRun: forceDryRun || opts.dryRun === true,
     ...(deps.projectionApplier === undefined ? {} : { projectionApplier: deps.projectionApplier }),
   });
diff --git a/packages/mosaic/src/commands/fleet-migration-command.ts b/packages/mosaic/src/commands/fleet-migration-command.ts
index 0c85a57e..907f16b2 100644
--- a/packages/mosaic/src/commands/fleet-migration-command.ts
+++ b/packages/mosaic/src/commands/fleet-migration-command.ts
@@ -1,5 +1,6 @@
 import { readFile } from 'node:fs/promises';
 import { join } from 'node:path';
+import { fleetAgentEnvDir, fleetRolesLocalDir } from '../fleet/brain-home.js';
 import type { Command } from 'commander';
 import {
   parseV1MigrationObservations,
@@ -120,11 +121,11 @@ export function registerFleetMigrationCommand(
           observations,
           personaDirs: {
             rolesDir: deps.rolesDir ?? join(mosaicHome, 'fleet', 'roles'),
-            overrideDir: deps.overrideDir ?? join(mosaicHome, 'fleet', 'roles.local'),
+            overrideDir: deps.overrideDir ?? fleetRolesLocalDir(mosaicHome),
           },
           environment: {
             mosaicHome,
-            agentEnvDir: join(mosaicHome, 'fleet', 'agents'),
+            agentEnvDir: fleetAgentEnvDir(mosaicHome),
           },
         });
         printJson(preview);
diff --git a/packages/mosaic/src/commands/fleet-personas.ts b/packages/mosaic/src/commands/fleet-personas.ts
index c3fe3fee..3333ea07 100644
--- a/packages/mosaic/src/commands/fleet-personas.ts
+++ b/packages/mosaic/src/commands/fleet-personas.ts
@@ -30,19 +30,21 @@ import { lstat, readFile, readdir, stat } from 'node:fs/promises';
 import { homedir } from 'node:os';
 import { basename, isAbsolute, join, sep } from 'node:path';
 import type { Command } from 'commander';
+import { fleetRolesLocalDir } from '../fleet/brain-home.js';
 
 function defaultMosaicHome(): string {
   return process.env['MOSAIC_HOME'] ?? join(homedir(), '.config', 'mosaic');
 }
 
-/** Baseline persona role contracts (reseeded on update). */
+/** Baseline persona role contracts (reseeded on update; config home — framework). */
 export function defaultRolesDir(mosaicHome = defaultMosaicHome()): string {
   return join(mosaicHome, 'fleet', 'roles');
 }
 
-/** PRESERVE-protected override layer (survives update; wins on merge). */
+/** PRESERVE-protected override layer (survives update; wins on merge).
+ * Brain home (`~/.mosaic/fleet/roles.local`) when a brain is active. */
 export function defaultOverrideDir(mosaicHome = defaultMosaicHome()): string {
-  return join(mosaicHome, 'fleet', 'roles.local');
+  return fleetRolesLocalDir(mosaicHome);
 }
 
 /**
diff --git a/packages/mosaic/src/commands/fleet-profiles.ts b/packages/mosaic/src/commands/fleet-profiles.ts
index 96899d9a..aaf82e26 100644
--- a/packages/mosaic/src/commands/fleet-profiles.ts
+++ b/packages/mosaic/src/commands/fleet-profiles.ts
@@ -25,6 +25,7 @@ import { homedir } from 'node:os';
 import { basename, join } from 'node:path';
 import type { Command } from 'commander';
 import YAML from 'yaml';
+import { fleetProfilesDir } from '../fleet/brain-home.js';
 import {
   defaultOverrideDir,
   extractClassesFromDir,
@@ -36,9 +37,10 @@ function defaultMosaicHome(): string {
   return process.env['MOSAIC_HOME'] ?? join(homedir(), '.config', 'mosaic');
 }
 
-/** Directory holding the seeded profile yaml files. */
+/** Directory holding the seeded profile yaml files — brain home when active
+ * (user working copies, committed), else the config home seed. */
 export function defaultProfilesDir(mosaicHome = defaultMosaicHome()): string {
-  return join(mosaicHome, 'fleet', 'profiles');
+  return fleetProfilesDir(mosaicHome);
 }
 
 /** Directory holding the persona role contracts. */
diff --git a/packages/mosaic/src/commands/fleet-regen-command.ts b/packages/mosaic/src/commands/fleet-regen-command.ts
index 6f478b0b..007b65d6 100644
--- a/packages/mosaic/src/commands/fleet-regen-command.ts
+++ b/packages/mosaic/src/commands/fleet-regen-command.ts
@@ -3,6 +3,7 @@ import { homedir } from 'node:os';
 import { join, relative, resolve } from 'node:path';
 import type { Command } from 'commander';
 import type { CommandRunner } from './fleet.js';
+import { fleetAgentEnvDir } from '../fleet/brain-home.js';
 import {
   applyPreparedGeneratedAgentEnvironmentProjection,
   prepareGeneratedAgentEnvironmentProjection,
@@ -153,7 +154,7 @@ export async function executeFleetRegen(
   options: FleetRegenOptions,
 ): Promise<FleetRegenResult> {
   const mosaicHome = defaultMosaicHome(deps);
-  const agentEnvDir = join(mosaicHome, 'fleet', 'agents');
+  const agentEnvDir = fleetAgentEnvDir(mosaicHome);
   const rosterPath = join(mosaicHome, 'fleet', 'roster.yaml');
   const readRoster = deps.readRoster ?? defaultReadRoster(deps, mosaicHome);
   const prepare = deps.prepareProjection ?? prepareGeneratedAgentEnvironmentProjection;
diff --git a/packages/mosaic/src/commands/fleet.ts b/packages/mosaic/src/commands/fleet.ts
index b77c6e3a..2bf0bab8 100644
--- a/packages/mosaic/src/commands/fleet.ts
+++ b/packages/mosaic/src/commands/fleet.ts
@@ -13,6 +13,7 @@ import {
 import { randomUUID } from 'node:crypto';
 import { homedir, hostname, userInfo } from 'node:os';
 import { dirname, join, resolve } from 'node:path';
+import { fleetAgentEnvDir } from '../fleet/brain-home.js';
 import { fileURLToPath } from 'node:url';
 import { spawn } from 'node:child_process';
 import * as readline from 'node:readline';
@@ -158,7 +159,7 @@ export function resolveFleetPaths(mosaicHome = defaultMosaicHome()): FleetPaths
     fleetToolsDir: join(mosaicHome, 'tools', 'fleet'),
     tmuxToolsDir: join(mosaicHome, 'tools', 'tmux'),
     systemdUserDir: join(homedir(), '.config', 'systemd', 'user'),
-    agentEnvDir: join(mosaicHome, 'fleet', 'agents'),
+    agentEnvDir: fleetAgentEnvDir(mosaicHome),
   };
 }
 
diff --git a/packages/mosaic/src/fleet/brain-home.spec.ts b/packages/mosaic/src/fleet/brain-home.spec.ts
new file mode 100644
index 00000000..a071d183
--- /dev/null
+++ b/packages/mosaic/src/fleet/brain-home.spec.ts
@@ -0,0 +1,114 @@
+import { mkdir, mkdtemp, rm } from 'node:fs/promises';
+import { homedir, tmpdir } from 'node:os';
+import { join } from 'node:path';
+import { afterEach, beforeEach, describe, expect, it } from 'vitest';
+import {
+  brainHomeIsActive,
+  fleetAgentEnvDir,
+  fleetProfilesDir,
+  fleetRolesLocalDir,
+  fleetStateDir,
+  resolveBrainHome,
+  type BrainHomeOptions,
+} from './brain-home.js';
+
+describe('fleet brain-home resolution', (): void => {
+  let cleanup: string | undefined;
+
+  const savedBrainEnv = process.env['MOSAIC_BRAIN_HOME'];
+
+  beforeEach((): void => {
+    delete process.env['MOSAIC_BRAIN_HOME'];
+  });
+
+  afterEach(async (): Promise<void> => {
+    if (savedBrainEnv === undefined) {
+      delete process.env['MOSAIC_BRAIN_HOME'];
+    } else {
+      process.env['MOSAIC_BRAIN_HOME'] = savedBrainEnv;
+    }
+    if (cleanup !== undefined) {
+      await rm(cleanup, { recursive: true, force: true });
+      cleanup = undefined;
+    }
+  });
+
+  async function makeTmp(): Promise<string> {
+    const root = await mkdtemp(join(tmpdir(), 'mosaic-brain-home-'));
+    cleanup = root;
+    return root;
+  }
+
+  it('MOSAIC_BRAIN_HOME env wins over every other signal', (): void => {
+    process.env['MOSAIC_BRAIN_HOME'] = '/explicit/brain';
+    expect(resolveBrainHome('/any/mosaic-home')).toBe('/explicit/brain');
+    expect(fleetAgentEnvDir('/any/mosaic-home')).toBe('/explicit/brain/fleet/agents');
+    expect(brainHomeIsActive('/any/mosaic-home')).toBe(true);
+  });
+
+  it('injected envBrainHome wins identically (test seam)', (): void => {
+    const opts: BrainHomeOptions = { envBrainHome: '/injected/brain' };
+    expect(resolveBrainHome('/any/mosaic-home', opts)).toBe('/injected/brain');
+    expect(fleetAgentEnvDir('/any/mosaic-home', opts)).toBe('/injected/brain/fleet/agents');
+  });
+
+  it('a non-default mosaicHome never adopts the canonical brain (hermetic legacy)', (): void => {
+    const mosaicHome = '/tmp/not-the-default-config-home';
+    expect(resolveBrainHome(mosaicHome)).toBe(mosaicHome);
+    expect(brainHomeIsActive(mosaicHome)).toBe(false);
+    expect(fleetAgentEnvDir(mosaicHome)).toBe(join(mosaicHome, 'fleet', 'agents'));
+  });
+
+  it('the default config home adopts the brain when it carries fleet/agents', async (): Promise<void> => {
+    const root = await makeTmp();
+    const brain = join(root, 'brain');
+    await mkdir(join(brain, 'fleet', 'agents'), { recursive: true });
+    const configHome = join(root, 'config', 'mosaic');
+    const opts: BrainHomeOptions = { homes: { brain, configDefault: configHome } };
+
+    expect(resolveBrainHome(configHome, opts)).toBe(brain);
+    expect(fleetAgentEnvDir(configHome, opts)).toBe(join(brain, 'fleet', 'agents'));
+    expect(fleetRolesLocalDir(configHome, opts)).toBe(join(brain, 'fleet', 'roles.local'));
+    expect(fleetProfilesDir(configHome, opts)).toBe(join(brain, 'fleet', 'profiles'));
+    expect(fleetStateDir(configHome, opts)).toBe(join(brain, 'fleet'));
+    expect(brainHomeIsActive(configHome, opts)).toBe(true);
+  });
+
+  it('the default config home stays legacy when no brain exists', async (): Promise<void> => {
+    const root = await makeTmp();
+    const configHome = join(root, 'config', 'mosaic');
+    const opts: BrainHomeOptions = {
+      homes: { brain: join(root, 'brain'), configDefault: configHome },
+    };
+
+    expect(resolveBrainHome(configHome, opts)).toBe(configHome);
+    expect(brainHomeIsActive(configHome, opts)).toBe(false);
+  });
+
+  it('an empty MOSAIC_BRAIN_HOME is ignored, not treated as set', (): void => {
+    process.env['MOSAIC_BRAIN_HOME'] = '   ';
+    expect(resolveBrainHome('/tmp/legacy-home')).toBe('/tmp/legacy-home');
+  });
+
+  it('adoption requires fleet/agents specifically, not any brain content', async (): Promise<void> => {
+    const root = await makeTmp();
+    const brain = join(root, 'brain');
+    await mkdir(join(brain, 'fleet'), { recursive: true }); // fleet without agents
+    const configHome = join(root, 'config', 'mosaic');
+    const opts: BrainHomeOptions = { homes: { brain, configDefault: configHome } };
+
+    expect(resolveBrainHome(configHome, opts)).toBe(configHome);
+  });
+
+  it('real-home control: a host brain is adopted only through the default home', (): void => {
+    // Control on the un-injected path: this host carries ~/.mosaic/fleet/agents,
+    // so the default config home resolves to the brain or legacy — both valid
+    // canonical endpoints — while a non-default home never adopts.
+    const defaultHome = join(homedir(), '.config', 'mosaic');
+    const resolved = resolveBrainHome(defaultHome);
+    expect([defaultHome, join(homedir(), '.mosaic')]).toContain(resolved);
+    expect(resolveBrainHome(join(homedir(), 'elsewhere', 'mosaic'))).toBe(
+      join(homedir(), 'elsewhere', 'mosaic'),
+    );
+  });
+});
diff --git a/packages/mosaic/src/fleet/brain-home.ts b/packages/mosaic/src/fleet/brain-home.ts
new file mode 100644
index 00000000..1c5fd689
--- /dev/null
+++ b/packages/mosaic/src/fleet/brain-home.ts
@@ -0,0 +1,76 @@
+import { existsSync } from 'node:fs';
+import { homedir } from 'node:os';
+import { join, resolve } from 'node:path';
+
+/**
+ * Overridable resolution inputs (tests inject tmp homes; production reads
+ * the environment and the real home directory).
+ */
+export interface BrainHomeOptions {
+  /** Explicit brain home; defaults to `MOSAIC_BRAIN_HOME`. */
+  readonly envBrainHome?: string;
+  /**
+   * Canonical homes used for adoption. Defaults derive from the real
+   * `homedir()`: `{ brain: ~/.mosaic, configDefault: ~/.config/mosaic }`.
+   */
+  readonly homes?: { readonly brain: string; readonly configDefault: string };
+}
+
+/**
+ * Brain-home resolution — the three-tree fleet split (stack canon
+ * `docs/STRUCTURE-CANON.md` §2, first carried by the USC estate brain):
+ *
+ *   config home (~/.config/mosaic)  framework templates + dispatch state:
+ *                                   fleet/roles (baseline), fleet/roster.yaml,
+ *                                   fleet/run (heartbeats), fleet/services
+ *   brain home  (~/.mosaic)         user-owned fleet state, committed:
+ *                                   fleet/agents/<seat>.env.*, fleet/roles.local,
+ *                                   fleet/profiles working copies
+ *
+ * Resolution order:
+ *   1. `MOSAIC_BRAIN_HOME` env (explicit, always wins)
+ *   2. canonical `~/.mosaic` — adopted ONLY when mosaicHome is the real
+ *      default config home AND `~/.mosaic/fleet/agents` exists. Custom
+ *      `--mosaic-home` values (tests, sandboxes, canaries) never trigger
+ *      adoption, keeping them hermetic and deterministic.
+ *   3. mosaicHome itself (legacy single-tree behavior).
+ */
+export function resolveBrainHome(mosaicHome: string, options: BrainHomeOptions = {}): string {
+  const explicit = options.envBrainHome ?? process.env['MOSAIC_BRAIN_HOME'];
+  if (explicit !== undefined && explicit.trim() !== '') {
+    return explicit;
+  }
+  const homes = options.homes ?? {
+    brain: join(homedir(), '.mosaic'),
+    configDefault: join(homedir(), '.config', 'mosaic'),
+  };
+  if (resolve(mosaicHome) !== resolve(homes.configDefault)) {
+    return mosaicHome;
+  }
+  return existsSync(join(homes.brain, 'fleet', 'agents')) ? homes.brain : mosaicHome;
+}
+
+/** True when fleet state resolves somewhere other than the config home. */
+export function brainHomeIsActive(mosaicHome: string, options: BrainHomeOptions = {}): boolean {
+  return resolve(resolveBrainHome(mosaicHome, options)) !== resolve(mosaicHome);
+}
+
+/** Fleet state root (brain home when active, else the config home). */
+export function fleetStateDir(mosaicHome: string, options: BrainHomeOptions = {}): string {
+  return join(resolveBrainHome(mosaicHome, options), 'fleet');
+}
+
+/** Seat launch envs — `<brainHome>/fleet/agents` when a brain is active. */
+export function fleetAgentEnvDir(mosaicHome: string, options: BrainHomeOptions = {}): string {
+  return join(fleetStateDir(mosaicHome, options), 'agents');
+}
+
+/** PRESERVE-protected persona override layer — `<brainHome>/fleet/roles.local`. */
+export function fleetRolesLocalDir(mosaicHome: string, options: BrainHomeOptions = {}): string {
+  return join(fleetStateDir(mosaicHome, options), 'roles.local');
+}
+
+/** System-type profiles (user working copies) — `<brainHome>/fleet/profiles`. */
+export function fleetProfilesDir(mosaicHome: string, options: BrainHomeOptions = {}): string {
+  return join(fleetStateDir(mosaicHome, options), 'profiles');
+}
diff --git a/packages/mosaic/src/fleet/fleet-reconciler.ts b/packages/mosaic/src/fleet/fleet-reconciler.ts
index 732c878d..60bbdadf 100644
--- a/packages/mosaic/src/fleet/fleet-reconciler.ts
+++ b/packages/mosaic/src/fleet/fleet-reconciler.ts
@@ -3,6 +3,7 @@ import { lstat, open, readFile, unlink, type FileHandle } from 'node:fs/promises
 import { randomUUID } from 'node:crypto';
 import { homedir } from 'node:os';
 import { join } from 'node:path';
+import { fleetAgentEnvDir } from './brain-home.js';
 import {
   applyPreparedAgentEnvironmentProjection,
   prepareAgentEnvironmentProjection,
@@ -617,7 +618,7 @@ function defaultPrepareProjections(
         (agent: FleetRosterV2Agent): Promise<PreparedAgentEnvironmentProjection> =>
           prepareAgentEnvironmentProjection({
             mosaicHome,
-            agentEnvDir: join(mosaicHome, 'fleet', 'agents'),
+            agentEnvDir: fleetAgentEnvDir(mosaicHome),
             agentName: agent.name,
             generated: projectRosterV2AgentGeneratedEnv(roster, agent),
           }),
diff --git a/packages/mosaic/src/fleet/generated-env-boundary.spec.ts b/packages/mosaic/src/fleet/generated-env-boundary.spec.ts
index c0c8a96e..09c9fd59 100644
--- a/packages/mosaic/src/fleet/generated-env-boundary.spec.ts
+++ b/packages/mosaic/src/fleet/generated-env-boundary.spec.ts
@@ -176,6 +176,52 @@ describe('generated fleet agent environment boundary', (): void => {
     expect((await stat(result.generatedPath)).mode & 0o777).toBe(0o600);
   });
 
+  it('brain home: accepts and writes projections under MOSAIC_BRAIN_HOME/fleet/agents', async (): Promise<void> => {
+    const savedBrainHome = process.env['MOSAIC_BRAIN_HOME'];
+    try {
+      cleanup = await mkdtemp(join(tmpdir(), 'mosaic-generated-env-'));
+      const mosaicHome = join(cleanup, 'config-home');
+      const brainHome = join(cleanup, 'brain');
+      const agentEnvDir = join(brainHome, 'fleet', 'agents');
+      process.env['MOSAIC_BRAIN_HOME'] = brainHome;
+
+      const result = await writeAgentEnvironmentProjection({
+        mosaicHome,
+        agentEnvDir,
+        agentName: 'coder0',
+        generated: generatedValues,
+      });
+
+      // Projection landed in the brain tree, not under the config home.
+      expect(result.generatedPath).toBe(join(agentEnvDir, 'coder0.env.generated'));
+      expect((await stat(join(brainHome, 'fleet'))).mode & 0o777).toBe(0o700);
+      expect((await stat(agentEnvDir)).mode & 0o777).toBe(0o700);
+      expect((await stat(result.generatedPath)).mode & 0o777).toBe(0o600);
+      await expect(stat(join(mosaicHome, 'fleet'))).rejects.toThrow();
+
+      // A config-home agentEnvDir is now REJECTED while the brain is active —
+      // the boundary must not silently split state across two trees.
+      let rejected: unknown;
+      try {
+        await writeAgentEnvironmentProjection({
+          mosaicHome,
+          agentEnvDir: join(mosaicHome, 'fleet', 'agents'),
+          agentName: 'coder1',
+          generated: { ...generatedValues, MOSAIC_AGENT_NAME: 'coder1' },
+        });
+      } catch (caught: unknown) {
+        rejected = caught;
+      }
+      expect(rejected).toBeInstanceOf(AgentEnvBoundaryError);
+    } finally {
+      if (savedBrainHome === undefined) {
+        delete process.env['MOSAIC_BRAIN_HOME'];
+      } else {
+        process.env['MOSAIC_BRAIN_HOME'] = savedBrainHome;
+      }
+    }
+  });
+
   it('regenerates desired keys, relocates safe legacy local data, and quarantines forbidden legacy input', async (): Promise<void> => {
     cleanup = await mkdtemp(join(tmpdir(), 'mosaic-generated-env-'));
     const mosaicHome = join(cleanup, 'mosaic');
diff --git a/packages/mosaic/src/fleet/generated-env-boundary.ts b/packages/mosaic/src/fleet/generated-env-boundary.ts
index cd849440..4db94203 100644
--- a/packages/mosaic/src/fleet/generated-env-boundary.ts
+++ b/packages/mosaic/src/fleet/generated-env-boundary.ts
@@ -2,6 +2,7 @@ import { createHash, randomUUID } from 'node:crypto';
 import { chmod, lstat, mkdir, readFile, rename, unlink, writeFile } from 'node:fs/promises';
 import { homedir } from 'node:os';
 import { dirname, join, resolve } from 'node:path';
+import { fleetAgentEnvDir, resolveBrainHome } from './brain-home.js';
 import { compareCodePoints } from './deterministic-order.js';
 
 export type AgentEnvironmentKind = 'generated' | 'local';
@@ -528,12 +529,15 @@ async function validatePrivateProjectionDirectory(
   mosaicHome: string,
   agentEnvDir: string,
 ): Promise<void> {
-  const fleetDir = join(mosaicHome, 'fleet');
-  const expectedAgentEnvDir = join(fleetDir, 'agents');
+  // Brain-home split (canon §2): seat envs live under the brain home's
+  // fleet/agents when a brain is active; roster + templates stay config-home.
+  const expectedAgentEnvDir = fleetAgentEnvDir(mosaicHome);
   if (resolve(agentEnvDir) !== resolve(expectedAgentEnvDir)) {
     throw new AgentEnvBoundaryError('unsafe-directory', '(directory)', agentEnvDir);
   }
-  await assertManagedDirectoryIfPresent(mosaicHome, false);
+  const stateHome = resolveBrainHome(mosaicHome);
+  const fleetDir = join(stateHome, 'fleet');
+  await assertManagedDirectoryIfPresent(stateHome, false);
   await assertManagedDirectoryIfPresent(fleetDir, false);
   await assertManagedDirectoryIfPresent(agentEnvDir, true);
 }
@@ -543,8 +547,9 @@ async function ensurePrivateProjectionDirectory(
   agentEnvDir: string,
 ): Promise<void> {
   await validatePrivateProjectionDirectory(mosaicHome, agentEnvDir);
-  const fleetDir = join(mosaicHome, 'fleet');
-  await ensureManagedDirectory(mosaicHome, false);
+  const stateHome = resolveBrainHome(mosaicHome);
+  const fleetDir = join(stateHome, 'fleet');
+  await ensureManagedDirectory(stateHome, false);
   await ensureManagedDirectory(fleetDir, false);
   await ensureManagedDirectory(agentEnvDir, true);
 }