diff --git a/model_tools.py b/model_tools.py
index 36cea8f304..b7dbb340b7 100644
--- a/model_tools.py
+++ b/model_tools.py
@@ -366,7 +366,7 @@ def get_tool_definitions(
 # because they need agent-level state (TodoStore, MemoryStore, etc.).
 # The registry still holds their schemas; dispatch just returns a stub error
 # so if something slips through, the LLM sees a sensible message.
-_AGENT_LOOP_TOOLS = {"todo", "memory", "session_search", "delegate_task"}
+_AGENT_LOOP_TOOLS = {"todo", "memory", "session_search", "delegate_task", "checkpoint"}
 _READ_SEARCH_TOOLS = {"read_file", "search_files"}
 
 
diff --git a/run_agent.py b/run_agent.py
index 6770f568c0..017812ac48 100644
--- a/run_agent.py
+++ b/run_agent.py
@@ -1561,6 +1561,11 @@ class AIAgent:
         # In-memory todo list for task planning (one per agent/session)
         from tools.todo_tool import TodoStore
         self._todo_store = TodoStore()
+
+        # Layer 4: Checkpoint store (session resumption across compression)
+        from agent.checkpoint_store import CheckpointStore
+        self._checkpoint_store = CheckpointStore()
+        self._checkpoint_store.garbage_collect()  # prune stale checkpoints on startup
         
         # Load config once for memory, skills, and compression sections
         try:
@@ -8351,6 +8356,19 @@ class AIAgent:
             )
         elif function_name == "delegate_task":
             return self._dispatch_delegate_task(function_args)
+        elif function_name == "checkpoint":
+            from tools.checkpoint_tool import checkpoint_tool as _checkpoint_tool
+            return _checkpoint_tool(
+                action=function_args.get("action"),
+                task=function_args.get("task"),
+                progress=function_args.get("progress"),
+                state=function_args.get("state"),
+                decisions=function_args.get("decisions"),
+                blocked=function_args.get("blocked"),
+                unresolved=function_args.get("unresolved"),
+                store=self._checkpoint_store,
+                agent=self,
+            )
         else:
             return handle_function_call(
                 function_name, function_args, effective_task_id,
@@ -8892,6 +8910,22 @@ class AIAgent:
                         spinner.stop(cute_msg)
                     elif self._should_emit_quiet_tool_messages():
                         self._vprint(f"  {cute_msg}")
+            elif function_name == "checkpoint":
+                from tools.checkpoint_tool import checkpoint_tool as _checkpoint_tool
+                function_result = _checkpoint_tool(
+                    action=function_args.get("action"),
+                    task=function_args.get("task"),
+                    progress=function_args.get("progress"),
+                    state=function_args.get("state"),
+                    decisions=function_args.get("decisions"),
+                    blocked=function_args.get("blocked"),
+                    unresolved=function_args.get("unresolved"),
+                    store=self._checkpoint_store,
+                    agent=self,
+                )
+                tool_duration = time.time() - tool_start_time
+                if self._should_emit_quiet_tool_messages():
+                    self._vprint(f"  {_get_cute_tool_message_impl('checkpoint', function_args, tool_duration, result=function_result)}")
             elif self._context_engine_tool_names and function_name in self._context_engine_tool_names:
                 # Context engine tools (lcm_grep, lcm_describe, lcm_expand, etc.)
                 spinner = None
diff --git a/tests/test_checkpoint_agent_dispatch.py b/tests/test_checkpoint_agent_dispatch.py
new file mode 100644
index 0000000000..6e48a8201d
--- /dev/null
+++ b/tests/test_checkpoint_agent_dispatch.py
@@ -0,0 +1,16 @@
+"""Verify that checkpoint is routed through the agent loop, not the registry."""
+import json
+import pytest
+from model_tools import handle_function_call, _AGENT_LOOP_TOOLS
+
+
+def test_checkpoint_is_agent_loop_tool():
+    """checkpoint must be in _AGENT_LOOP_TOOLS so it gets agent-level state."""
+    assert "checkpoint" in _AGENT_LOOP_TOOLS
+
+
+def test_checkpoint_registry_dispatch_returns_error():
+    """Calling handle_function_call for checkpoint should return agent-loop error."""
+    result = handle_function_call("checkpoint", {"action": "read"})
+    data = json.loads(result)
+    assert "must be handled" in data["error"].lower()
\ No newline at end of file