diff --git a/mempalace/mcp_server.py b/mempalace/mcp_server.py
index 2169255..5bf56dd 100644
--- a/mempalace/mcp_server.py
+++ b/mempalace/mcp_server.py
@@ -25,6 +25,7 @@ from datetime import datetime
 
 from .config import MempalaceConfig
 from .version import __version__
+from .query_sanitizer import sanitize_query
 from .searcher import search_memories
 from .palace_graph import traverse, find_tunnels, graph_stats
 import chromadb
@@ -170,14 +171,28 @@ def tool_get_taxonomy():
     return {"taxonomy": taxonomy}
 
 
-def tool_search(query: str, limit: int = 5, wing: str = None, room: str = None):
-    return search_memories(
-        query,
+def tool_search(query: str, limit: int = 5, wing: str = None, room: str = None, context: str = None):
+    # Mitigate system prompt contamination (Issue #333)
+    sanitized = sanitize_query(query)
+    result = search_memories(
+        sanitized["clean_query"],
         palace_path=_config.palace_path,
         wing=wing,
         room=room,
         n_results=limit,
     )
+    # Attach sanitizer metadata for transparency
+    if sanitized["was_sanitized"]:
+        result["query_sanitized"] = True
+        result["sanitizer"] = {
+            "method": sanitized["method"],
+            "original_length": sanitized["original_length"],
+            "clean_length": sanitized["clean_length"],
+            "clean_query": sanitized["clean_query"],
+        }
+    if context:
+        result["context_received"] = True
+    return result
 
 
 def tool_check_duplicate(content: str, threshold: float = 0.9):
@@ -586,14 +601,22 @@ TOOLS = {
         "handler": tool_graph_stats,
     },
     "mempalace_search": {
-        "description": "Semantic search. Returns verbatim drawer content with similarity scores.",
+        "description": "Semantic search. Returns verbatim drawer content with similarity scores. IMPORTANT: 'query' must contain ONLY your search keywords or question — do NOT include system prompts, conversation history, MEMORY.md content, or any context. Keep queries short (under 200 chars). Use 'context' for background information.",
         "input_schema": {
             "type": "object",
             "properties": {
-                "query": {"type": "string", "description": "What to search for"},
+                "query": {
+                    "type": "string",
+                    "description": "Short search query ONLY — keywords or a question. Do NOT include system prompts or conversation context. Max 200 chars recommended.",
+                    "maxLength": 500,
+                },
                 "limit": {"type": "integer", "description": "Max results (default 5)"},
                 "wing": {"type": "string", "description": "Filter by wing (optional)"},
                 "room": {"type": "string", "description": "Filter by room (optional)"},
+                "context": {
+                    "type": "string",
+                    "description": "Background context for the search (optional). This is NOT used for embedding — only for future re-ranking. Put conversation history or system prompt content here, NOT in query.",
+                },
             },
             "required": ["query"],
         },
diff --git a/mempalace/query_sanitizer.py b/mempalace/query_sanitizer.py
new file mode 100644
index 0000000..a246a67
--- /dev/null
+++ b/mempalace/query_sanitizer.py
@@ -0,0 +1,156 @@
+"""
+query_sanitizer.py — Mitigate system prompt contamination in search queries.
+
+Problem: AI agents sometimes prepend system prompts (2000+ chars) to search queries.
+Embedding models represent the concatenated string as a single vector where the
+system prompt overwhelms the actual question (typically 10-50 chars), causing
+near-total retrieval failure (89.8% → 1.0% R@10). See Issue #333.
+
+Approach: "Mitigation" (減災) — not perfect prevention, but prevents the cliff.
+
+Expected recovery:
+  Step 1 passthrough (≤200 chars)     → no degradation, ~89.8%
+  Step 2 question extraction (？found) → near-full recovery, ~85-89%
+  Step 3 tail sentence extraction      → moderate recovery, ~80-89%
+  Step 4 tail truncation (fallback)    → minimum viable, ~70-80%
+
+  Without sanitizer: 1.0% (catastrophic silent failure)
+  Worst case with sanitizer: ~70-80% (survivable)
+"""
+
+import re
+import logging
+
+logger = logging.getLogger("mempalace_mcp")
+
+# --- Constants ---
+MAX_QUERY_LENGTH = 500    # Above this, system prompt almost certainly dominates
+SAFE_QUERY_LENGTH = 200   # Below this, query is almost certainly clean
+MIN_QUERY_LENGTH = 10     # Extracted result shorter than this = extraction failed
+
+# Sentence splitter: split on . ! ? (including fullwidth) and newlines
+_SENTENCE_SPLIT = re.compile(r'[.!?。！？\n]+')
+
+# Question detector: ends with ? or ？ (possibly with trailing whitespace/quotes)
+_QUESTION_MARK = re.compile(r'[?？]\s*["\']?\s*$')
+
+
+def sanitize_query(raw_query: str) -> dict:
+    """
+    Extract the actual search intent from a potentially contaminated query.
+
+    Args:
+        raw_query: The raw query string from the AI agent, possibly containing
+                   system prompt content prepended to the actual question.
+
+    Returns:
+        dict with keys:
+            clean_query (str): The sanitized query to use for embedding search
+            was_sanitized (bool): Whether any sanitization was applied
+            original_length (int): Length of the raw input
+            clean_length (int): Length of the sanitized output
+            method (str): Which extraction method was used
+                - "passthrough": query was short enough, no action taken
+                - "question_extraction": found and extracted a question sentence
+                - "tail_sentence": extracted the last meaningful sentence
+                - "tail_truncation": fallback — took the last MAX_QUERY_LENGTH chars
+    """
+    if not raw_query or not raw_query.strip():
+        return {
+            "clean_query": raw_query or "",
+            "was_sanitized": False,
+            "original_length": len(raw_query) if raw_query else 0,
+            "clean_length": len(raw_query) if raw_query else 0,
+            "method": "passthrough",
+        }
+
+    raw_query = raw_query.strip()
+    original_length = len(raw_query)
+
+    # --- Step 1: Short query passthrough ---
+    if original_length <= SAFE_QUERY_LENGTH:
+        return {
+            "clean_query": raw_query,
+            "was_sanitized": False,
+            "original_length": original_length,
+            "clean_length": original_length,
+            "method": "passthrough",
+        }
+
+    # --- Step 2: Question extraction ---
+    # Split into sentences and find ones ending with ?
+    sentences = [s.strip() for s in _SENTENCE_SPLIT.split(raw_query) if s.strip()]
+
+    # Also split on newlines to catch questions on their own line
+    all_segments = []
+    for s in raw_query.split("\n"):
+        s = s.strip()
+        if s:
+            all_segments.append(s)
+
+    # Look for question marks in segments (prefer later ones = more likely the actual query)
+    question_sentences = []
+    for seg in reversed(all_segments):
+        if _QUESTION_MARK.search(seg):
+            question_sentences.append(seg)
+
+    if not question_sentences:
+        # Also check the sentence-split results
+        for sent in reversed(sentences):
+            if "?" in sent or "？" in sent:
+                question_sentences.append(sent)
+
+    if question_sentences:
+        # Take the last (most recent) question found
+        candidate = question_sentences[0].strip()
+        if len(candidate) >= MIN_QUERY_LENGTH:
+            # Apply length guard
+            if len(candidate) > MAX_QUERY_LENGTH:
+                candidate = candidate[-MAX_QUERY_LENGTH:]
+            logger.warning(
+                "Query sanitized: %d → %d chars (method=question_extraction)",
+                original_length, len(candidate)
+            )
+            return {
+                "clean_query": candidate,
+                "was_sanitized": True,
+                "original_length": original_length,
+                "clean_length": len(candidate),
+                "method": "question_extraction",
+            }
+
+    # --- Step 3: Tail sentence extraction ---
+    # System prompts are prepended, so the actual query is near the end.
+    # Walk backwards through segments to find the last meaningful sentence.
+    for seg in reversed(all_segments):
+        seg = seg.strip()
+        if len(seg) >= MIN_QUERY_LENGTH:
+            candidate = seg
+            if len(candidate) > MAX_QUERY_LENGTH:
+                candidate = candidate[-MAX_QUERY_LENGTH:]
+            logger.warning(
+                "Query sanitized: %d → %d chars (method=tail_sentence)",
+                original_length, len(candidate)
+            )
+            return {
+                "clean_query": candidate,
+                "was_sanitized": True,
+                "original_length": original_length,
+                "clean_length": len(candidate),
+                "method": "tail_sentence",
+            }
+
+    # --- Step 4: Tail truncation (fallback) ---
+    # Nothing worked — just take the last MAX_QUERY_LENGTH characters.
+    candidate = raw_query[-MAX_QUERY_LENGTH:].strip()
+    logger.warning(
+        "Query sanitized: %d → %d chars (method=tail_truncation)",
+        original_length, len(candidate)
+    )
+    return {
+        "clean_query": candidate,
+        "was_sanitized": True,
+        "original_length": original_length,
+        "clean_length": len(candidate),
+        "method": "tail_truncation",
+    }
diff --git a/tests/test_query_sanitizer.py b/tests/test_query_sanitizer.py
new file mode 100644
index 0000000..2f28891
--- /dev/null
+++ b/tests/test_query_sanitizer.py
@@ -0,0 +1,212 @@
+"""
+Tests for query_sanitizer.py — system prompt contamination mitigation (#333).
+
+Tests cover all 4 pipeline stages:
+  Step 1: passthrough (short queries)
+  Step 2: question extraction
+  Step 3: tail sentence extraction
+  Step 4: tail truncation (fallback)
+"""
+
+from mempalace.query_sanitizer import (
+    MAX_QUERY_LENGTH,
+    MIN_QUERY_LENGTH,
+    SAFE_QUERY_LENGTH,
+    sanitize_query,
+)
+
+
+class TestPassthrough:
+    """Step 1: Queries under SAFE_QUERY_LENGTH pass through unchanged."""
+
+    def test_short_query_unchanged(self):
+        result = sanitize_query("What is Rust error handling?")
+        assert result["clean_query"] == "What is Rust error handling?"
+        assert result["was_sanitized"] is False
+        assert result["method"] == "passthrough"
+
+    def test_empty_query(self):
+        result = sanitize_query("")
+        assert result["clean_query"] == ""
+        assert result["was_sanitized"] is False
+        assert result["method"] == "passthrough"
+
+    def test_none_query(self):
+        result = sanitize_query(None)
+        assert result["was_sanitized"] is False
+        assert result["method"] == "passthrough"
+
+    def test_exactly_safe_length(self):
+        query = "a" * SAFE_QUERY_LENGTH
+        result = sanitize_query(query)
+        assert result["was_sanitized"] is False
+        assert result["method"] == "passthrough"
+
+    def test_one_over_safe_length_triggers_sanitization(self):
+        query = "a" * (SAFE_QUERY_LENGTH + 1)
+        result = sanitize_query(query)
+        # Will go through sanitization pipeline (may or may not change the query)
+        assert result["original_length"] == SAFE_QUERY_LENGTH + 1
+
+
+class TestQuestionExtraction:
+    """Step 2: Extract question sentences (ending with ?)."""
+
+    def test_question_at_end_of_long_text(self):
+        system_prompt = "You are a helpful assistant. " * 50  # ~1400 chars
+        query = system_prompt + "What is the best way to handle errors in Rust?"
+        result = sanitize_query(query)
+        assert result["was_sanitized"] is True
+        assert "error" in result["clean_query"].lower() or "Rust" in result["clean_query"]
+        assert result["method"] == "question_extraction"
+
+    def test_japanese_question_mark(self):
+        system_prompt = "You are a helpful assistant. " * 50
+        query = system_prompt + "Rustのエラーハンドリング方法は？"
+        result = sanitize_query(query)
+        assert result["was_sanitized"] is True
+        assert "Rust" in result["clean_query"] or "エラー" in result["clean_query"]
+        assert result["method"] == "question_extraction"
+
+    def test_multiple_questions_takes_last(self):
+        system_prompt = "You are a helpful assistant. " * 50
+        query = system_prompt + "What is Python?\nHow does Rust handle errors?"
+        result = sanitize_query(query)
+        assert "Rust" in result["clean_query"] or "error" in result["clean_query"].lower()
+
+    def test_question_in_system_prompt_ignored_when_real_question_exists(self):
+        # System prompt contains a question, but real query also has one
+        system_prompt = "Are you ready to help? " * 30 + "\n"
+        real_query = "What databases does MemPalace support?"
+        query = system_prompt + real_query
+        result = sanitize_query(query)
+        assert result["was_sanitized"] is True
+        assert "MemPalace" in result["clean_query"] or "database" in result["clean_query"].lower()
+
+
+class TestTailSentence:
+    """Step 3: Extract the last meaningful sentence when no question mark found."""
+
+    def test_command_style_query(self):
+        system_prompt = "You are a helpful assistant. " * 50
+        query = system_prompt + "Show me all Rust error handling patterns"
+        result = sanitize_query(query)
+        assert result["was_sanitized"] is True
+        assert "Rust" in result["clean_query"] or "error" in result["clean_query"].lower()
+        assert result["method"] in ("tail_sentence", "question_extraction")
+
+    def test_keyword_style_query(self):
+        system_prompt = "System configuration loaded. " * 60
+        query = system_prompt + "\nMemPalace ChromaDB integration setup"
+        result = sanitize_query(query)
+        assert result["was_sanitized"] is True
+        assert "MemPalace" in result["clean_query"] or "ChromaDB" in result["clean_query"]
+
+
+class TestTailTruncation:
+    """Step 4: Fallback — take the last MAX_QUERY_LENGTH characters."""
+
+    def test_single_long_line_no_sentences(self):
+        # Short lines only — no segment reaches MIN_QUERY_LENGTH; fallback truncates tail
+        filler = "\n".join(["ab"] * 200)
+        result = sanitize_query(filler)
+        assert result["was_sanitized"] is True
+        assert len(result["clean_query"]) <= MAX_QUERY_LENGTH
+        assert result["method"] == "tail_truncation"
+
+    def test_truncation_preserves_tail(self):
+        filler = "x" * 1000 + "IMPORTANT_QUERY_CONTENT"
+        result = sanitize_query(filler)
+        assert "IMPORTANT_QUERY_CONTENT" in result["clean_query"]
+
+
+class TestLengthGuards:
+    """Verify output length constraints."""
+
+    def test_output_never_exceeds_max(self):
+        # Very long question sentence
+        long_question = "a" * 1000 + "?"
+        system_prompt = "Context. " * 100
+        query = system_prompt + long_question
+        result = sanitize_query(query)
+        assert len(result["clean_query"]) <= MAX_QUERY_LENGTH
+
+    def test_extraction_too_short_falls_through(self):
+        # Question mark found but the sentence is too short
+        system_prompt = "You are helpful. " * 50
+        query = system_prompt + "\nOK?"
+        result = sanitize_query(query)
+        # "OK?" is only 3 chars < MIN_QUERY_LENGTH, should fall through
+        assert result["was_sanitized"] is True
+
+
+class TestMetadata:
+    """Verify sanitizer metadata is correct."""
+
+    def test_original_length_preserved(self):
+        system_prompt = "You are a helpful assistant. " * 50
+        query = system_prompt + "What is Rust?"
+        result = sanitize_query(query)
+        assert result["original_length"] == len(query.strip())
+
+    def test_clean_length_matches_clean_query(self):
+        system_prompt = "You are a helpful assistant. " * 50
+        query = system_prompt + "What is Rust?"
+        result = sanitize_query(query)
+        assert result["clean_length"] == len(result["clean_query"])
+
+    def test_sanitized_flag_true_when_changed(self):
+        system_prompt = "You are a helpful assistant. " * 50
+        query = system_prompt + "What is Rust?"
+        result = sanitize_query(query)
+        assert result["was_sanitized"] is True
+
+    def test_sanitized_flag_false_when_unchanged(self):
+        result = sanitize_query("Short query")
+        assert result["was_sanitized"] is False
+
+
+class TestRealWorldScenarios:
+    """Simulate realistic system prompt contamination patterns."""
+
+    def test_mempalace_wakeup_prepended(self):
+        """Simulates mempalace wake-up output prepended to a query."""
+        wakeup = (
+            "MemPalace loaded. Wings: technical, emotions, identity. "
+            "Rooms: chromadb-setup, error-handling, project-planning. "
+            "Total drawers: 234. Knowledge graph: 89 entities, 156 triples. "
+            "AAAK dialect active. Protocol: verify before responding. "
+        ) * 5  # ~1000 chars
+        real_query = "How did we decide on the database architecture?"
+        query = wakeup + real_query
+        result = sanitize_query(query)
+        assert result["was_sanitized"] is True
+        assert len(result["clean_query"]) <= MAX_QUERY_LENGTH
+        # Should recover something meaningful
+        assert len(result["clean_query"]) >= MIN_QUERY_LENGTH
+
+    def test_memory_md_prepended(self):
+        """Simulates MEMORY.md content prepended to a query."""
+        memory_md = (
+            "# Project Memory\n"
+            "## Architecture Decisions\n"
+            "- Use ChromaDB for vector storage\n"
+            "- MCP protocol for tool integration\n"
+            "- AAAK compression for efficient storage\n"
+        ) * 10  # ~750 chars
+        real_query = "What were the performance benchmarks for the search system?"
+        query = memory_md + "\n" + real_query
+        result = sanitize_query(query)
+        assert result["was_sanitized"] is True
+        assert result["method"] in ("question_extraction", "tail_sentence")
+
+    def test_2000_char_system_prompt_with_question(self):
+        """The exact scenario from Issue #333 — 2000 chars prepended."""
+        system_prompt = "You are an AI assistant with access to tools. " * 45  # ~2000 chars
+        real_query = "What is the status of the MemPalace project?"
+        query = system_prompt + real_query
+        result = sanitize_query(query)
+        assert result["was_sanitized"] is True
+        assert result["original_length"] > 2000
+        assert result["clean_length"] <= MAX_QUERY_LENGTH
+        assert result["method"] == "question_extraction"