diff --git a/overlay/packages/opencode/src/session/agent/local.ts b/overlay/packages/opencode/src/session/agent/local.ts
index 50414c5..7038c61 100644
--- a/overlay/packages/opencode/src/session/agent/local.ts
+++ b/overlay/packages/opencode/src/session/agent/local.ts
@@ -1,8 +1,9 @@
 import { spawn, type ChildProcessWithoutNullStreams } from "node:child_process"
 import { randomUUID } from "node:crypto"
-import { existsSync } from "node:fs"
+import { existsSync, readFileSync, unlinkSync } from "node:fs"
 import { homedir } from "node:os"
 import { join } from "node:path"
+import { setTimeout as sleep } from "node:timers/promises"
 
 export type LocalAgentKind = "claude" | "codex" | "opencode" | "hermes"
 
@@ -28,6 +29,12 @@ export type LocalAgentRecord = {
   // True when the agent runs interactively in its own terminal window: no
   // stdout/stderr is captured and stdin cannot be messaged.
   visible?: boolean
+  // PID of the command running inside a visible terminal, when known. Killing
+  // this process/group lets the terminal close once the command exits.
+  terminalPid?: number
+  // Linux visible-terminal launches write the command PID here from inside the
+  // terminal because many emulator launcher processes exit immediately.
+  terminalPidFile?: string
   stdout: string
   stderr: string
   // Characters trimmed from the front of each buffer once it exceeds
@@ -264,6 +271,8 @@ export function respawnLocalAgent(
   record.command = spec.command
   record.args = spec.args
   record.visible = false
+  record.terminalPid = undefined
+  discardTerminalPidFile(record)
   const child = spawn(spec.command, spec.args, {
     cwd: record.workspace,
     env: process.env,
@@ -336,9 +345,103 @@ export function readLocalAgentOutput(
   }
 }
 
-export function stopLocalAgent(handle: string): boolean {
+function markVisibleExited(record: LocalAgentRecord, signal: NodeJS.Signals | null): void {
+  record.visible = false
+  record.exitedAt = new Date().toISOString()
+  record.exitCode = null
+  record.signal = signal
+}
+
+// Remove the terminal PID file from tmp and forget it. Safe to call when no
+// file is tracked; swallows unlink errors (already gone, or never written).
+function discardTerminalPidFile(record: LocalAgentRecord): void {
+  if (!record.terminalPidFile) return
+  try {
+    unlinkSync(record.terminalPidFile)
+  } catch {}
+  record.terminalPidFile = undefined
+}
+
+function readTerminalPidFile(record: LocalAgentRecord): number | undefined {
+  if (!record.terminalPidFile) return undefined
+  try {
+    const pid = Number.parseInt(readFileSync(record.terminalPidFile, "utf8").trim(), 10)
+    if (!Number.isSafeInteger(pid) || pid <= 0) return undefined
+    record.pid = pid
+    record.terminalPid = pid
+    discardTerminalPidFile(record)
+    return pid
+  } catch {
+    return undefined
+  }
+}
+
+async function resolveVisibleTerminalPid(record: LocalAgentRecord, timeoutMs: number): Promise<number | undefined> {
+  if (record.terminalPid != null) return record.terminalPid
+  const deadline = Date.now() + timeoutMs
+  do {
+    const pid = readTerminalPidFile(record)
+    if (pid != null) return pid
+    if (!record.terminalPidFile) return undefined
+    await sleep(50)
+  } while (Date.now() < deadline)
+  return readTerminalPidFile(record)
+}
+
+function processExists(pid: number): boolean {
+  try {
+    process.kill(pid, 0)
+    return true
+  } catch (error) {
+    return error instanceof Error && "code" in error && error.code !== "ESRCH"
+  }
+}
+
+async function waitForProcessExit(pid: number, timeoutMs: number): Promise<boolean> {
+  const deadline = Date.now() + timeoutMs
+  do {
+    if (!processExists(pid)) return true
+    await sleep(50)
+  } while (Date.now() < deadline)
+  return !processExists(pid)
+}
+
+function signalVisiblePid(pid: number): boolean {
+  try {
+    process.kill(-pid, "SIGTERM")
+    return true
+  } catch {
+    try {
+      process.kill(pid, "SIGTERM")
+      return true
+    } catch {
+      return false
+    }
+  }
+}
+
+// Close a visible terminal by terminating the foreground command running inside
+// it. Linux launches track that command via a PID file so server-style terminal
+// emulators don't leave us holding a short-lived launcher PID. The record only
+// becomes reusable after the tracked process is observed gone.
+async function closeVisibleTerminal(record: LocalAgentRecord): Promise<boolean> {
+  const pid = await resolveVisibleTerminalPid(record, 1000)
+  if (pid == null) return false
+  if (!processExists(pid)) {
+    markVisibleExited(record, null)
+    return true
+  }
+  if (!signalVisiblePid(pid)) return false
+  if (!(await waitForProcessExit(pid, 1500))) return false
+  markVisibleExited(record, "SIGTERM")
+  return true
+}
+
+export async function stopLocalAgent(handle: string): Promise<boolean> {
   const record = agents.get(handle)
-  if (!record?.process) return false
+  if (!record) return false
+  if (record.visible) return closeVisibleTerminal(record)
+  if (!record.process) return false
   return record.process.kill("SIGTERM")
 }
 
@@ -353,6 +456,7 @@ export function registerVisibleAgent(params: {
   command: string
   args: string[]
   pid?: number
+  pidFile?: string
   sessionId?: string
 }): LocalAgentRecord {
   const record: LocalAgentRecord = {
@@ -366,6 +470,8 @@ export function registerVisibleAgent(params: {
     startedAt: new Date().toISOString(),
     sessionId: params.sessionId,
     visible: true,
+    terminalPid: params.pid,
+    terminalPidFile: params.pidFile,
     stdout: "",
     stderr: "",
     stdoutDropped: 0,
diff --git a/overlay/packages/opencode/src/session/agent/terminal.ts b/overlay/packages/opencode/src/session/agent/terminal.ts
index 3c591ea..2e51b77 100644
--- a/overlay/packages/opencode/src/session/agent/terminal.ts
+++ b/overlay/packages/opencode/src/session/agent/terminal.ts
@@ -4,12 +4,23 @@
 // known emulator found on PATH per platform.
 
 import { spawn, spawnSync } from "node:child_process"
-import { basename, delimiter, join } from "node:path"
+import { randomUUID } from "node:crypto"
 import { existsSync } from "node:fs"
+import { tmpdir } from "node:os"
+import { basename, delimiter, join } from "node:path"
 
 export type TerminalLaunch = {
   ok: boolean
   terminal?: string
+  // PID of the command running inside the visible terminal, when known at
+  // launch time. This is intentionally not the emulator launcher PID because
+  // common terminals hand work to a server process and then exit.
+  pid?: number
+  // On Linux the visible command writes its PID here from inside the terminal;
+  // callers can read it later if it was not available before this function
+  // returned. Undefined on macOS/Windows where closing the window is not yet
+  // supported reliably.
+  pidFile?: string
   error?: string
 }
 
@@ -70,7 +81,11 @@ function shellQuote(token: string): string {
   return `'${token.replace(/'/g, `'\\''`)}'`
 }
 
-function launchDetached(argv: string[], cwd: string): TerminalLaunch {
+function withPidCapture(argv: string[], pidFile: string): string[] {
+  return ["sh", "-c", 'pidfile=$1; shift; printf "%s\\n" "$$" > "$pidfile"; exec "$@"', "athena-terminal", pidFile, ...argv]
+}
+
+function launchDetached(argv: string[], cwd: string, pidFile?: string): TerminalLaunch {
   try {
     const child = spawn(argv[0]!, argv.slice(1), {
       cwd,
@@ -80,7 +95,7 @@ function launchDetached(argv: string[], cwd: string): TerminalLaunch {
     })
     child.on("error", () => {})
     child.unref()
-    return { ok: true, terminal: basename(argv[0]!) }
+    return { ok: true, terminal: basename(argv[0]!), pidFile }
   } catch (error) {
     return { ok: false, error: error instanceof Error ? error.message : String(error) }
   }
@@ -115,5 +130,6 @@ export function openVisibleTerminal(argv: string[], cwd: string): TerminalLaunch
       error: "No terminal emulator found on PATH (set ATHENA_TERMINAL to your terminal command).",
     }
   }
-  return launchDetached(emulatorArgv(candidates[0]!, argv, cwd), cwd)
+  const pidFile = join(tmpdir(), `athena-terminal-${randomUUID()}.pid`)
+  return launchDetached(emulatorArgv(candidates[0]!, withPidCapture(argv, pidFile), cwd), cwd, pidFile)
 }
diff --git a/overlay/packages/opencode/src/tool/agent-local.ts b/overlay/packages/opencode/src/tool/agent-local.ts
index df833ce..05e0598 100644
--- a/overlay/packages/opencode/src/tool/agent-local.ts
+++ b/overlay/packages/opencode/src/tool/agent-local.ts
@@ -80,6 +80,8 @@ export const AgentSpawnTool = tool({
         command: spec.command,
         args: spec.args,
         sessionId: spec.sessionId,
+        pid: launch.pid,
+        pidFile: launch.pidFile,
       })
       const note = spec.promptInjected
         ? `The task prompt was pre-submitted.`
@@ -87,7 +89,9 @@ export const AgentSpawnTool = tool({
       return {
         title: "Agent opened in terminal",
         metadata: { handle: record.handle, terminal: launch.terminal },
-        output: `${render(record)}\nOpened in a new ${launch.terminal} window. ${note} Output is not captured for visible agents.`,
+        output: `${render(record)}\nOpened in a new ${launch.terminal} window. ${note} Output is not captured for visible agents.${
+          launch.pid || launch.pidFile ? ` Close the window with agent_stop ${record.handle}.` : ""
+        }`,
       }
     }
     const record = spawnLocalAgent({ agent, task: args.task, workspace })
@@ -146,10 +150,14 @@ export const AgentTakeoverTool = tool({
         return { title: "Terminal launch failed", metadata: { error: true }, output: launch.error ?? "Could not open a terminal window." }
       }
       record.visible = true
+      record.terminalPid = launch.pid
+      record.terminalPidFile = launch.pidFile
       return {
         title: "Session opened in terminal",
         metadata: { handle: record.handle, sessionId, terminal: launch.terminal },
-        output: `Resumed ${record.agent} session ${sessionId} in a new ${launch.terminal} window.`,
+        output: `Resumed ${record.agent} session ${sessionId} in a new ${launch.terminal} window.${
+          launch.pid || launch.pidFile ? ` Close it later with agent_stop ${record.handle}.` : ""
+        }`,
       }
     }
     GlobalBus.emit("event", {
@@ -224,13 +232,13 @@ export const AgentMessageTool = tool({
 })
 
 export const AgentStopTool = tool({
-  description: "Stop a running local agent spawned by Athena Code. Use when the user asks to stop, kill, or terminate a specific spawned agent handle.",
+  description: "Stop a local agent spawned by Athena Code. Kills a headless agent process, or closes the window of an agent opened in a visible terminal (on Linux/BSD). Use when the user asks to stop, kill, terminate, or close a specific spawned agent handle.",
   args: {
     handle: tool.schema.string().describe('Agent handle, for example "claude#1" or "codex#1".'),
   },
   async execute(args) {
     const record = getLocalAgent(args.handle)
-    const ok = stopLocalAgent(args.handle)
+    const ok = await stopLocalAgent(args.handle)
     return { title: ok ? "Agent stopped" : "Agent not running", metadata: { handle: args.handle, ok }, output: record ? render(record) : `${args.handle} does not exist.` }
   },
 })
diff --git a/test/agent-local.test.ts b/test/agent-local.test.ts
index d695223..4cb6c0e 100644
--- a/test/agent-local.test.ts
+++ b/test/agent-local.test.ts
@@ -1,5 +1,6 @@
 import { test, expect } from "bun:test"
-import { mkdtempSync } from "node:fs"
+import { spawn } from "node:child_process"
+import { mkdtempSync, writeFileSync } from "node:fs"
 import { tmpdir } from "node:os"
 import { join } from "node:path"
 import {
@@ -15,8 +16,10 @@ import {
   resolveLocalAgentSessionId,
   respawnLocalAgent,
   spawnLocalAgentCommand,
+  stopLocalAgent,
   waitLocalAgent,
 } from "../overlay/packages/opencode/src/session/agent/local"
+import { openVisibleTerminal } from "../overlay/packages/opencode/src/session/agent/terminal"
 
 function workspace(prefix: string): string {
   return mkdtempSync(join(tmpdir(), prefix))
@@ -251,6 +254,90 @@ test("visible agents are listed but not resumed headless", async () => {
   expect((await continueLocalAgent(record.handle, "hello")).status).toBe("terminal")
 })
 
+test("stopLocalAgent keeps untracked visible terminals blocked", async () => {
+  const record = registerVisibleAgent({
+    agent: "claude",
+    task: "visible run",
+    workspace: workspace("athagent-"),
+    command: "claude",
+    args: ["visible run"],
+    sessionId: "uuid-2",
+  })
+
+  expect(await stopLocalAgent(record.handle)).toBe(false)
+  expect(record.visible).toBe(true)
+  expect(record.exitedAt).toBeUndefined()
+  expect(localAgentTakeoverBlockReason(record)).toBe("terminal")
+})
+
+test("stopLocalAgent closes visible agents with a tracked pid", async () => {
+  const child = spawn(process.execPath, ["-e", "setInterval(() => {}, 1000)"], {
+    detached: true,
+    stdio: "ignore",
+  })
+  const pid = child.pid!
+  const closed = new Promise<void>((resolve) => child.once("close", () => resolve()))
+  const record = registerVisibleAgent({
+    agent: "claude",
+    task: "visible run",
+    workspace: workspace("athagent-"),
+    command: process.execPath,
+    args: [],
+    pid,
+    sessionId: "uuid-3",
+  })
+
+  try {
+    expect(await stopLocalAgent(record.handle)).toBe(true)
+    await closed
+    expect(record.visible).toBe(false)
+    expect(record.exitedAt).toBeDefined()
+    expect(record.signal).toBe("SIGTERM")
+  } finally {
+    try {
+      process.kill(-pid, "SIGKILL")
+    } catch {}
+  }
+})
+
+test("openVisibleTerminal tracks Linux command pid through a pid file", async () => {
+  if (process.platform !== "linux") return
+  const dir = workspace("athagent-terminal-")
+  const terminal = join(dir, "fake-terminal")
+  writeFileSync(terminal, '#!/bin/sh\nif [ "$1" = "-e" ]; then shift; fi\nexec "$@"\n', { mode: 0o755 })
+
+  const previousAthenaTerminal = process.env.ATHENA_TERMINAL
+  const previousTerminal = process.env.TERMINAL
+  process.env.ATHENA_TERMINAL = terminal
+  delete process.env.TERMINAL
+  try {
+    const launch = openVisibleTerminal([process.execPath, "-e", "setInterval(() => {}, 1000)"], dir)
+    expect(launch.ok).toBe(true)
+    expect(launch.pid).toBeUndefined()
+    expect(launch.pidFile).toBeDefined()
+
+    const record = registerVisibleAgent({
+      agent: "claude",
+      task: "visible run",
+      workspace: dir,
+      command: process.execPath,
+      args: [],
+      pid: launch.pid,
+      pidFile: launch.pidFile,
+      sessionId: "uuid-4",
+    })
+
+    expect(await stopLocalAgent(record.handle)).toBe(true)
+    expect(record.terminalPid).toBeGreaterThan(0)
+    expect(record.visible).toBe(false)
+  } finally {
+    if (previousAthenaTerminal === undefined) delete process.env.ATHENA_TERMINAL
+    else process.env.ATHENA_TERMINAL = previousAthenaTerminal
+    if (previousTerminal === undefined) delete process.env.TERMINAL
+    else process.env.TERMINAL = previousTerminal
+  }
+})
+
 test("one-shot agents get stdin closed so stdin-draining CLIs exit", async () => {
   const record = spawnLocalAgentCommand({
     agent: "codex",