diff --git a/src/agent/runner.ts b/src/agent/runner.ts
index 90f5416a..9ae9bf27 100644
--- a/src/agent/runner.ts
+++ b/src/agent/runner.ts
@@ -23,6 +23,7 @@ export class Agent {
   private readonly skillManager?: SkillManager;
   private readonly contextWindowGuard: ContextWindowGuardResult;
   private readonly debug: boolean;
+  private initialized = false;
 
   /** Current session ID */
   readonly sessionId: string;
@@ -172,31 +173,6 @@ export class Agent {
     }
     this.agent.setTools(tools);
 
-    const restoredMessages = this.session.loadMessages();
-    if (restoredMessages.length > 0) {
-      if (this.debug) {
-        console.error(`[debug] Restoring ${restoredMessages.length} messages from session`);
-        for (const msg of restoredMessages) {
-          const msgAny = msg as any;
-          const content = Array.isArray(msgAny.content)
-            ? msgAny.content.map((c: any) => c.type || "text").join(", ")
-            : typeof msgAny.content;
-          console.error(`[debug]   ${msg.role}: ${content}`);
-          if (Array.isArray(msgAny.content)) {
-            for (const block of msgAny.content) {
-              if (block.type === "tool_use") {
-                console.error(`[debug]     tool_use id: ${block.id}, name: ${block.name}`);
-              }
-              if (block.type === "tool_result") {
-                console.error(`[debug]     tool_result tool_use_id: ${block.tool_use_id}`);
-              }
-            }
-          }
-        }
-      }
-      this.agent.replaceMessages(restoredMessages);
-    }
-
     this.session.saveMeta({
       provider: this.agent.state.model?.provider,
       model: this.agent.state.model?.id,
@@ -216,6 +192,34 @@ export class Agent {
   }
 
   async run(prompt: string): Promise<AgentRunResult> {
+    if (!this.initialized) {
+      await this.session.repairIfNeeded((msg) => console.error(msg));
+      const restoredMessages = this.session.loadMessages();
+      if (restoredMessages.length > 0) {
+        if (this.debug) {
+          console.error(`[debug] Restoring ${restoredMessages.length} messages from session`);
+          for (const msg of restoredMessages) {
+            const msgAny = msg as any;
+            const content = Array.isArray(msgAny.content)
+              ? msgAny.content.map((c: any) => c.type || "text").join(", ")
+              : typeof msgAny.content;
+            console.error(`[debug]   ${msg.role}: ${content}`);
+            if (Array.isArray(msgAny.content)) {
+              for (const block of msgAny.content) {
+                if (block.type === "tool_use") {
+                  console.error(`[debug]     tool_use id: ${block.id}, name: ${block.name}`);
+                }
+                if (block.type === "tool_result") {
+                  console.error(`[debug]     tool_result tool_use_id: ${block.tool_use_id}`);
+                }
+              }
+            }
+          }
+        }
+        this.agent.replaceMessages(restoredMessages);
+      }
+      this.initialized = true;
+    }
     this.output.state.lastAssistantText = "";
     await this.agent.prompt(prompt);
     return { text: this.output.state.lastAssistantText, error: this.agent.state.error };
diff --git a/src/agent/session/session-manager.ts b/src/agent/session/session-manager.ts
index e6793b36..a820072a 100644
--- a/src/agent/session/session-manager.ts
+++ b/src/agent/session/session-manager.ts
@@ -1,9 +1,11 @@
 import type { AgentMessage } from "@mariozechner/pi-agent-core";
 import { getModel, type Model } from "@mariozechner/pi-ai";
 import type { SessionEntry, SessionMeta } from "./types.js";
-import { appendEntry, readEntries, writeEntries } from "./storage.js";
+import { appendEntry, readEntries, resolveSessionPath, writeEntries } from "./storage.js";
 import { compactMessages, compactMessagesAsync } from "./compaction.js";
 import { credentialManager } from "../credentials.js";
+import { repairSessionFileIfNeeded, type RepairReport } from "./session-file-repair.js";
+import { sanitizeToolCallInputs, sanitizeToolUseResultPairing } from "./session-transcript-repair.js";
 
 /** Get Kimi model for summarization (use a cheaper model than k2-thinking) */
 function getSummaryModel(): Model<any> {
@@ -140,11 +142,19 @@ export class SessionManager {
     return readEntries(this.sessionId, { baseDir: this.baseDir });
   }
 
+  async repairIfNeeded(warn?: (message: string) => void): Promise<RepairReport> {
+    const filePath = resolveSessionPath(this.sessionId, { baseDir: this.baseDir });
+    return repairSessionFileIfNeeded({ sessionFile: filePath, warn });
+  }
+
   loadMessages(): AgentMessage[] {
     const entries = this.loadEntries();
-    return entries
+    let messages = entries
       .filter((entry) => entry.type === "message")
       .map((entry) => entry.message);
+    messages = sanitizeToolCallInputs(messages);
+    messages = sanitizeToolUseResultPairing(messages);
+    return messages;
   }
 
   loadMeta(): SessionMeta | undefined {
diff --git a/src/agent/session/storage.ts b/src/agent/session/storage.ts
index b219fd95..63915783 100644
--- a/src/agent/session/storage.ts
+++ b/src/agent/session/storage.ts
@@ -3,6 +3,7 @@ import { existsSync, mkdirSync, readFileSync } from "fs";
 import { appendFile, writeFile } from "fs/promises";
 import type { SessionEntry } from "./types.js";
 import { DATA_DIR } from "../../shared/index.js";
+import { acquireSessionWriteLock } from "./session-write-lock.js";
 
 export type SessionStorageOptions = {
   baseDir?: string | undefined;
@@ -50,7 +51,12 @@ export async function appendEntry(
 ) {
   ensureSessionDir(sessionId, options);
   const filePath = resolveSessionPath(sessionId, options);
-  await appendFile(filePath, `${JSON.stringify(entry)}\n`, "utf8");
+  const lock = await acquireSessionWriteLock({ sessionFile: filePath });
+  try {
+    await appendFile(filePath, `${JSON.stringify(entry)}\n`, "utf8");
+  } finally {
+    await lock.release();
+  }
 }
 
 export async function writeEntries(
@@ -60,6 +66,11 @@ export async function writeEntries(
 ) {
   ensureSessionDir(sessionId, options);
   const filePath = resolveSessionPath(sessionId, options);
-  const content = entries.map((entry) => JSON.stringify(entry)).join("\n");
-  await writeFile(filePath, content ? `${content}\n` : "", "utf8");
+  const lock = await acquireSessionWriteLock({ sessionFile: filePath });
+  try {
+    const content = entries.map((entry) => JSON.stringify(entry)).join("\n");
+    await writeFile(filePath, content ? `${content}\n` : "", "utf8");
+  } finally {
+    await lock.release();
+  }
 }