diff --git a/packages/core/src/code_assist/converter.test.ts b/packages/core/src/code_assist/converter.test.ts
index ab040fe6..0b71e33f 100644
--- a/packages/core/src/code_assist/converter.test.ts
+++ b/packages/core/src/code_assist/converter.test.ts
@@ -17,6 +17,7 @@ import {
   GenerateContentResponse,
   FinishReason,
   BlockedReason,
+  Part,
 } from '@google/genai';
 
 describe('converter', () => {
@@ -349,5 +350,94 @@ 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 7ca17386..89f5b525 100644
--- a/packages/core/src/code_assist/converter.ts
+++ b/packages/core/src/code_assist/converter.ts
@@ -189,13 +189,18 @@ function toContent(content: ContentUnion): Content {
     };
   }
   if ('parts' in content) {
-    // it's a Content
-    return content;
+    // it's a Content - process parts to handle thought filtering
+    return {
+      ...content,
+      parts: content.parts
+        ? toParts(content.parts.filter((p) => p != null))
+        : [],
+    };
   }
   // it's a Part
   return {
     role: 'user',
-    parts: [content as Part],
+    parts: [toPart(content as Part)],
   };
 }
 
@@ -208,6 +213,41 @@ function toPart(part: PartUnion): Part {
     // it's a string
     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;
 }