diff --git a/conductor/tracks/thinking_trace_handling_20260313/plan.md b/conductor/tracks/thinking_trace_handling_20260313/plan.md
index 7a90ca6..98c4811 100644
--- a/conductor/tracks/thinking_trace_handling_20260313/plan.md
+++ b/conductor/tracks/thinking_trace_handling_20260313/plan.md
@@ -7,14 +7,13 @@
 - [x] Task: Implement: Update parsing logic in `src/ai_client.py` or a dedicated utility to extract segments from raw provider responses.
 - [ ] Task: Conductor - User Manual Verification 'Phase 1: Core Parsing & Model Update' (Protocol in workflow.md)
 - [ ] Task: Write Tests: Verify that `ProjectManager` correctly serializes and deserializes messages with thinking segments to/from TOML history files.
-- [ ] Task: Implement: Update `src/project_manager.py` to handle the new `ChatMessage` schema during session save/load.
-- [ ] Task: Implement: Ensure `src/aggregate.py` or relevant context builders include thinking traces in the "Discussion History" sent back to the AI.
-- [ ] Task: Conductor - User Manual Verification 'Phase 2: Persistence & History Integration' (Protocol in workflow.md)
+- [ ] Task: Conductor - User Manual Verification 'Phase 1: Core Parsing & Model Update' (Protocol in workflow.md)
 
-## Phase 3: GUI Rendering - Comms & Discussion
-- [ ] Task: Write Tests: Verify the GUI rendering logic correctly handles messages with and without thinking segments.
-- [ ] Task: Implement: Create a reusable `_render_thinking_trace` helper in `src/gui_2.py` using a collapsible header (e.g., `imgui.collapsing_header`).
-- [ ] Task: Implement: Integrate the thinking trace renderer into the **Comms History** panel in `src/gui_2.py`.
+## Phase 2: Persistence & History Integration
+- [x] Task: Write Tests: Verify that `ProjectManager` correctly serializes and deserializes messages with thinking segments to/from TOML history files.
+- [x] Task: Implement: Update `src/project_manager.py` to handle the new `ChatMessage` schema during session save/load.
+- [x] Task: Implement: Ensure `src/aggregate.py` or relevant context builders include thinking traces in the "Discussion History" sent back to the AI.
+- [ ] Task: Conductor - User Manual Verification 'Phase 2: Persistence & History Integration' (Protocol in workflow.md)
 - [ ] Task: Implement: Integrate the thinking trace renderer into the **Discussion Hub** message loop in `src/gui_2.py`.
 - [ ] Task: Conductor - User Manual Verification 'Phase 3: GUI Rendering - Comms & Discussion' (Protocol in workflow.md)
 
diff --git a/tests/test_thinking_persistence.py b/tests/test_thinking_persistence.py
new file mode 100644
index 0000000..c30f61c
--- /dev/null
+++ b/tests/test_thinking_persistence.py
@@ -0,0 +1,94 @@
+import pytest
+import tempfile
+import os
+from pathlib import Path
+from src import project_manager
+from src.models import ThinkingSegment
+
+
+def test_save_and_load_history_with_thinking_segments():
+    with tempfile.TemporaryDirectory() as tmpdir:
+        project_path = Path(tmpdir) / "test_project"
+        project_path.mkdir()
+
+        project_file = project_path / "test_project.toml"
+        project_file.write_text("[project]\nname = 'test'\n")
+
+        history_data = {
+            "entries": [
+                {
+                    "role": "AI",
+                    "content": "Here's the response",
+                    "thinking_segments": [
+                        {"content": "Let me think about this...", "marker": "thinking"}
+                    ],
+                    "ts": "2026-03-13T10:00:00",
+                    "collapsed": False,
+                },
+                {
+                    "role": "User",
+                    "content": "Hello",
+                    "ts": "2026-03-13T09:00:00",
+                    "collapsed": False,
+                },
+            ]
+        }
+
+        project_manager.save_project(
+            {"project": {"name": "test"}}, project_file, disc_data=history_data
+        )
+
+        loaded = project_manager.load_history(project_file)
+
+        assert "entries" in loaded
+        assert len(loaded["entries"]) == 2
+
+        ai_entry = loaded["entries"][0]
+        assert ai_entry["role"] == "AI"
+        assert ai_entry["content"] == "Here's the response"
+        assert "thinking_segments" in ai_entry
+        assert len(ai_entry["thinking_segments"]) == 1
+        assert (
+            ai_entry["thinking_segments"][0]["content"] == "Let me think about this..."
+        )
+
+        user_entry = loaded["entries"][1]
+        assert user_entry["role"] == "User"
+        assert "thinking_segments" not in user_entry
+
+
+def test_entry_to_str_with_thinking():
+    entry = {
+        "role": "AI",
+        "content": "Response text",
+        "thinking_segments": [{"content": "Thinking...", "marker": "thinking"}],
+        "ts": "2026-03-13T10:00:00",
+    }
+    result = project_manager.entry_to_str(entry)
+    assert "@2026-03-13T10:00:00" in result
+    assert "AI:" in result
+    assert "Response text" in result
+
+
+def test_str_to_entry_with_thinking():
+    raw = "@2026-03-13T10:00:00\nAI:\nResponse text"
+    roles = ["User", "AI", "Vendor API", "System", "Reasoning"]
+    result = project_manager.str_to_entry(raw, roles)
+    assert result["role"] == "AI"
+    assert result["content"] == "Response text"
+    assert "ts" in result
+
+
+def test_clean_nones_removes_thinking():
+    entry = {"role": "AI", "content": "Test", "thinking_segments": None, "ts": None}
+    cleaned = project_manager.clean_nones(entry)
+    assert "thinking_segments" not in cleaned
+    assert "ts" not in cleaned
+
+
+if __name__ == "__main__":
+    test_save_and_load_history_with_thinking_segments()
+    test_entry_to_str_with_thinking()
+    test_str_to_entry_with_thinking()
+    test_clean_nones_removes_thinking()
+    print("All project_manager thinking tests passed!")