diff --git a/packages/core/src/code_assist/converter.test.ts b/packages/core/src/code_assist/converter.test.ts
index 83309412038..67e6123a931 100644
--- a/packages/core/src/code_assist/converter.test.ts
+++ b/packages/core/src/code_assist/converter.test.ts
@@ -17,7 +17,6 @@ import {
   BlockedReason,
   type ContentListUnion,
   type GenerateContentParameters,
-  type Part,
 } from '@google/genai';
 
 describe('converter', () => {
@@ -392,94 +391,5 @@ describe('converter', () => {
         { role: 'user', parts: [{ text: 'string 2' }] },
       ]);
     });
-
-    it('should convert thought parts to text parts for API compatibility', () => {
-      const contentWithThought: ContentListUnion = {
-        role: 'model',
-        parts: [
-          { text: 'regular text' },
-          { thought: 'thinking about the problem' } as Part & {
-            thought: string;
-          },
-          { text: 'more text' },
-        ],
-      };
-      expect(toContents(contentWithThought)).toEqual([
-        {
-          role: 'model',
-          parts: [
-            { text: 'regular text' },
-            { text: '[Thought: thinking about the problem]' },
-            { text: 'more text' },
-          ],
-        },
-      ]);
-    });
-
-    it('should combine text and thought for text parts with thoughts', () => {
-      const contentWithTextAndThought: ContentListUnion = {
-        role: 'model',
-        parts: [
-          {
-            text: 'Here is my response',
-            thought: 'I need to be careful here',
-          } as Part & { thought: string },
-        ],
-      };
-      expect(toContents(contentWithTextAndThought)).toEqual([
-        {
-          role: 'model',
-          parts: [
-            {
-              text: 'Here is my response\n[Thought: I need to be careful here]',
-            },
-          ],
-        },
-      ]);
-    });
-
-    it('should preserve non-thought properties while removing thought', () => {
-      const contentWithComplexPart: ContentListUnion = {
-        role: 'model',
-        parts: [
-          {
-            functionCall: { name: 'calculate', args: { x: 5, y: 10 } },
-            thought: 'Performing calculation',
-          } as Part & { thought: string },
-        ],
-      };
-      expect(toContents(contentWithComplexPart)).toEqual([
-        {
-          role: 'model',
-          parts: [
-            {
-              functionCall: { name: 'calculate', args: { x: 5, y: 10 } },
-            },
-          ],
-        },
-      ]);
-    });
-
-    it('should convert invalid text content to valid text part with thought', () => {
-      const contentWithInvalidText: ContentListUnion = {
-        role: 'model',
-        parts: [
-          {
-            text: 123, // Invalid - should be string
-            thought: 'Processing number',
-          } as Part & { thought: string; text: number },
-        ],
-      };
-      expect(toContents(contentWithInvalidText)).toEqual([
-        {
-          role: 'model',
-          parts: [
-            {
-              text: '123\n[Thought: Processing number]',
-            },
-          ],
-        },
-      ]);
-    });
   });
 });
diff --git a/packages/core/src/code_assist/converter.ts b/packages/core/src/code_assist/converter.ts
index 005a8cf85d6..fe52afc8a90 100644
--- a/packages/core/src/code_assist/converter.ts
+++ b/packages/core/src/code_assist/converter.ts
@@ -244,40 +244,6 @@ function toPart(part: PartUnion): Part {
     return { text: part };
   }
 
-  // Handle thought parts for CountToken API compatibility
-  // The CountToken API expects parts to have certain required "oneof" fields initialized,
-  // but thought parts don't conform to this schema and cause API failures
-  if ('thought' in part && part.thought) {
-    const thoughtText = `[Thought: ${part.thought}]`;
-
-    const newPart = { ...part };
-    delete (newPart as Record<string, unknown>)['thought'];
-
-    const hasApiContent =
-      'functionCall' in newPart ||
-      'functionResponse' in newPart ||
-      'inlineData' in newPart ||
-      'fileData' in newPart;
-
-    if (hasApiContent) {
-      // It's a functionCall or other non-text part. Just strip the thought.
-      return newPart;
-    }
-
-    // If no other valid API content, this must be a text part.
-    // Combine existing text (if any) with the thought, preserving other properties.
-    const text = (newPart as { text?: unknown }).text;
-    const existingText = text ? String(text) : '';
-    const combinedText = existingText
-      ? `${existingText}\n${thoughtText}`
-      : thoughtText;
-
-    return {
-      ...newPart,
-      text: combinedText,
-    };
-  }
-
   return part;
 }
 
diff --git a/packages/core/src/utils/sessionUtils.test.ts b/packages/core/src/utils/sessionUtils.test.ts
index d132087ee82..1341cf37234 100644
--- a/packages/core/src/utils/sessionUtils.test.ts
+++ b/packages/core/src/utils/sessionUtils.test.ts
@@ -7,6 +7,7 @@ import { describe, it, expect } from 'vitest';
 import { convertSessionToClientHistory } from './sessionUtils.js';
 import { type ConversationRecord } from '../services/chatRecordingService.js';
 import { CoreToolCallStatus } from '../scheduler/types.js';
+import { toContents } from '../code_assist/converter.js';
 
 describe('convertSessionToClientHistory', () => {
   it('should convert a simple conversation without tool calls', () => {
@@ -182,4 +183,60 @@ describe('convertSessionToClientHistory', () => {
       },
     ]);
   });
+
+  it('integration: should ensure thoughts survive conversion back to API format without string mutation on session resume', () => {
+    // 1. A simulated conversation pulled from storage (like session resume)
+    const messages: ConversationRecord['messages'] = [
+      {
+        id: '1',
+        type: 'user',
+        timestamp: '2024-01-01T10:00:00Z',
+        content: 'Hello, can you help me?',
+      },
+      {
+        id: '2',
+        type: 'gemini',
+        timestamp: '2024-01-01T10:01:00Z',
+        content: 'AI Response',
+        thoughts: [
+          {
+            subject: 'Thinking',
+            description: 'I need to process this',
+            timestamp: '2024-01-01T10:00:50Z',
+          },
+        ],
+      },
+      {
+        id: '3',
+        type: 'user',
+        timestamp: '2024-01-01T10:02:00Z',
+        content: 'This is the first message after session resume.',
+      },
+    ];
+
+    // 2. convertSessionToClientHistory (what GeminiChat uses to load history internally)
+    const history = convertSessionToClientHistory(messages);
+
+    // 3. toContents (what the CodeAssist API / external AI provider uses internally to format network requests)
+    const generatedContents = toContents(history);
+
+    // 4. Assert that we don't accidentally mutate or inject '[Thought: true]' as string text.
+    expect(generatedContents).toEqual([
+      {
+        role: 'user',
+        parts: [{ text: 'Hello, can you help me?' }],
+      },
+      {
+        role: 'model',
+        parts: [
+          { text: '**Thinking** I need to process this', thought: true },
+          { text: 'AI Response' },
+        ],
+      },
+      {
+        role: 'user',
+        parts: [{ text: 'This is the first message after session resume.' }],
+      },
+    ]);
+  });
 });