MCP Architecture Deep Dive: How It Really Works

Model Context Protocol isn't just another API standard - it's a carefully architected system designed for high-performance AI integration. This technical deep dive explores MCP's architecture, from low-level protocol details to production deployment patterns.

Protocol Stack Overview

MCP follows a layered architecture that separates concerns and enables flexible deployment scenarios. Understanding this stack is crucial for architecting robust MCP integrations.

Layer Responsibilities

Core Components

MCP's architecture centers around two primary components that handle different aspects of the protocol implementation.

MCP Client Architecture

class MCPClient {
  private transport: Transport;
  private capabilities: ServerCapabilities;
  private sessionId: string;
  
  constructor(transport: Transport) {
    this.transport = transport;
    this.sessionId = generateSessionId();
  }
  
  async connect(): Promise<void> {
    await this.transport.connect();
    await this.handshake();
    await this.discoverCapabilities();
  }
  
  async callTool(
    name: string, 
    arguments: Record<string, any>
  ): Promise<ToolResult> {
    const request: ToolCallRequest = {
      method: "tools/call",
      params: { name, arguments }
    };
    
    return await this.sendRequest(request);
  }
  
  private async handshake(): Promise<void> {
    const initRequest = {
      method: "initialize",
      params: {
        protocolVersion: "1.0",
        capabilities: {
          sampling: {}
        },
        clientInfo: {
          name: "my-client",
          version: "1.0.0"
        }
      }
    };
    
    await this.sendRequest(initRequest);
  }
}

MCP Server Architecture

class MCPServer {
  private tools: Map<string, Tool> = new Map();
  private resources: Map<string, Resource> = new Map();
  private middleware: Middleware[] = [];
  
  registerTool(tool: Tool): void {
    this.tools.set(tool.name, tool);
  }
  
  async handleRequest(request: MCPRequest): Promise<MCPResponse> {
    // Apply middleware
    for (const mw of this.middleware) {
      request = await mw.preProcess(request);
    }
    
    switch (request.method) {
      case "tools/call":
        return await this.executeTool(request);
      case "resources/read":
        return await this.readResource(request);
      case "tools/list":
        return this.listTools();
      default:
        throw new MCPError("Method not found", -32601);
    }
  }
  
  private async executeTool(
    request: ToolCallRequest
  ): Promise<ToolResult> {
    const tool = this.tools.get(request.params.name);
    if (!tool) {
      throw new MCPError("Tool not found", -32602);
    }
    
    // Validate arguments
    await this.validateArguments(tool.schema, request.params.arguments);
    
    // Check permissions
    await this.checkPermissions(request, tool);
    
    // Execute tool
    return await tool.execute(request.params.arguments);
  }
}

Message Flow & Lifecycle

Understanding MCP's message flow is essential for debugging and optimizing integrations. Here's how a typical tool execution unfolds:

Initialization Sequence

// 1. Initialize Request
{
  "jsonrpc": "2.0",
  "id": 1,
  "method": "initialize",
  "params": {
    "protocolVersion": "1.0",
    "capabilities": {
      "sampling": {}
    },
    "clientInfo": {
      "name": "claude-desktop",
      "version": "1.0.0"
    }
  }
}

// 2. Initialize Response
{
  "jsonrpc": "2.0",
  "id": 1,
  "result": {
    "protocolVersion": "1.0",
    "capabilities": {
      "tools": {},
      "resources": {}
    },
    "serverInfo": {
      "name": "filesystem-server",
      "version": "1.0.0"
    }
  }
}

// 3. Initialized Notification
{
  "jsonrpc": "2.0",
  "method": "notifications/initialized"
}

Tool Execution Lifecycle

Transport Layer

MCP's transport-agnostic design enables deployment across diverse environments. Each transport has specific characteristics and use cases.

STDIO Transport

Ideal for local processes and command-line tools. Provides low-latency communication via standard input/output streams.

class StdioTransport implements Transport {
  private process: ChildProcess;
  
  async connect(): Promise<void> {
    this.process = spawn('node', ['mcp-server.js'], {
      stdio: ['pipe', 'pipe', 'inherit']
    });
    
    this.process.stdout.on('data', this.handleMessage.bind(this));
  }
  
  async send(message: MCPMessage): Promise<void> {
    const serialized = JSON.stringify(message) + '\n';
    this.process.stdin.write(serialized);
  }
  
  private handleMessage(data: Buffer): void {
    const lines = data.toString().split('\n');
    for (const line of lines) {
      if (line.trim()) {
        const message = JSON.parse(line);
        this.emit('message', message);
      }
    }
  }
}

HTTP Transport

Perfect for web-based implementations and remote servers. Supports both synchronous request/response and webhook patterns.

class HttpTransport implements Transport {
  private baseUrl: string;
  private httpClient: HttpClient;
  
  constructor(baseUrl: string) {
    this.baseUrl = baseUrl;
    this.httpClient = new HttpClient({
      timeout: 30000,
      retries: 3
    });
  }
  
  async send(message: MCPMessage): Promise<MCPResponse> {
    const response = await this.httpClient.post(
      `${this.baseUrl}/mcp`, 
      message,
      {
        headers: {
          'Content-Type': 'application/json',
          'X-MCP-Version': '1.0'
        }
      }
    );
    
    return response.data;
  }
}

WebSocket Integration

Enables real-time bidirectional communication with persistent connections and automatic reconnection.

class WebSocketTransport implements Transport {
  private ws: WebSocket;
  private reconnectAttempts = 0;
  private maxReconnectAttempts = 5;
  
  async connect(url: string): Promise<void> {
    return new Promise((resolve, reject) => {
      this.ws = new WebSocket(url);
      
      this.ws.onopen = () => {
        this.reconnectAttempts = 0;
        resolve();
      };
      
      this.ws.onmessage = (event) => {
        const message = JSON.parse(event.data);
        this.emit('message', message);
      };
      
      this.ws.onclose = () => {
        this.handleReconnect();
      };
    });
  }
  
  private async handleReconnect(): Promise<void> {
    if (this.reconnectAttempts < this.maxReconnectAttempts) {
      this.reconnectAttempts++;
      const delay = Math.pow(2, this.reconnectAttempts) * 1000;
      
      setTimeout(() => {
        this.connect(this.url);
      }, delay);
    }
  }
}

Security Model

MCP implements a multi-layered security approach that balances functionality with protection against various attack vectors.

Capability-Based Security

Servers expose only approved capabilities, and clients can only access explicitly granted functions.

class SecurityMiddleware {
  private allowedTools: Set<string>;
  private rateLimiter: RateLimiter;
  
  constructor(config: SecurityConfig) {
    this.allowedTools = new Set(config.allowedTools);
    this.rateLimiter = new RateLimiter({
      windowMs: 60000,  // 1 minute
      maxRequests: 100  // per client
    });
  }
  
  async preProcess(request: MCPRequest): Promise<MCPRequest> {
    // Rate limiting
    const clientId = this.extractClientId(request);
    await this.rateLimiter.checkLimit(clientId);
    
    // Tool access control
    if (request.method === 'tools/call') {
      const toolName = request.params.name;
      if (!this.allowedTools.has(toolName)) {
        throw new MCPError('Tool not allowed', -32603);
      }
    }
    
    // Argument sanitization
    return this.sanitizeArguments(request);
  }
  
  private sanitizeArguments(request: MCPRequest): MCPRequest {
    if (request.params?.arguments) {
      // Remove potentially dangerous patterns
      request.params.arguments = this.sanitizeObject(
        request.params.arguments
      );
    }
    return request;
  }
  
  private sanitizeObject(obj: any): any {
    const sanitized = {};
    
    for (const [key, value] of Object.entries(obj)) {
      // Prevent path traversal
      if (typeof value === 'string') {
        if (value.includes('../') || value.includes('..\\')) {
          throw new MCPError('Path traversal detected', -32602);
        }
      }
      
      // Recursive sanitization
      if (typeof value === 'object' && value !== null) {
        sanitized[key] = this.sanitizeObject(value);
      } else {
        sanitized[key] = value;
      }
    }
    
    return sanitized;
  }
}

Rate Limiting & Resource Protection

class RateLimiter {
  private windows: Map<string, Window> = new Map();
  
  constructor(private config: RateLimitConfig) {}
  
  async checkLimit(clientId: string): Promise<void> {
    const now = Date.now();
    const window = this.getOrCreateWindow(clientId, now);
    
    // Sliding window algorithm
    const windowStart = now - this.config.windowMs;
    window.requests = window.requests.filter(
      timestamp => timestamp > windowStart
    );
    
    if (window.requests.length >= this.config.maxRequests) {
      throw new MCPError('Rate limit exceeded', 429);
    }
    
    window.requests.push(now);
  }
  
  private getOrCreateWindow(clientId: string, now: number): Window {
    if (!this.windows.has(clientId)) {
      this.windows.set(clientId, { requests: [] });
    }
    return this.windows.get(clientId)!;
  }
}

Performance & Optimization

Production MCP implementations require careful attention to performance characteristics and optimization strategies.

Connection Pooling

For high-throughput scenarios, connection pooling reduces overhead and improves resource utilization.

class ConnectionPool {
  private pool: Connection[] = [];
  private activeConnections: Set<Connection> = new Set();
  private maxConnections: number;
  
  constructor(config: PoolConfig) {
    this.maxConnections = config.maxConnections || 10;
  }
  
  async getConnection(): Promise<Connection> {
    // Return available connection from pool
    if (this.pool.length > 0) {
      const connection = this.pool.pop()!;
      this.activeConnections.add(connection);
      return connection;
    }
    
    // Create new connection if under limit
    if (this.activeConnections.size < this.maxConnections) {
      const connection = await this.createConnection();
      this.activeConnections.add(connection);
      return connection;
    }
    
    // Wait for available connection
    return await this.waitForConnection();
  }
  
  releaseConnection(connection: Connection): void {
    this.activeConnections.delete(connection);
    
    if (connection.isHealthy()) {
      this.pool.push(connection);
    } else {
      connection.close();
    }
  }
}

Message Batching

Optimize throughput by batching multiple requests when possible.

class BatchProcessor {
  private batch: MCPRequest[] = [];
  private batchTimeout: NodeJS.Timeout | null = null;
  private readonly maxBatchSize = 10;
  private readonly batchTimeoutMs = 100;
  
  async enqueue(request: MCPRequest): Promise<MCPResponse> {
    return new Promise((resolve, reject) => {
      this.batch.push({
        ...request,
        resolve,
        reject
      });
      
      // Auto-flush on size
      if (this.batch.length >= this.maxBatchSize) {
        this.flush();
      }
      
      // Auto-flush on timeout
      if (!this.batchTimeout) {
        this.batchTimeout = setTimeout(() => {
          this.flush();
        }, this.batchTimeoutMs);
      }
    });
  }
  
  private async flush(): Promise<void> {
    if (this.batch.length === 0) return;
    
    const currentBatch = this.batch.splice(0);
    
    if (this.batchTimeout) {
      clearTimeout(this.batchTimeout);
      this.batchTimeout = null;
    }
    
    try {
      const responses = await this.processBatch(currentBatch);
      
      currentBatch.forEach((request, index) => {
        request.resolve(responses[index]);
      });
    } catch (error) {
      currentBatch.forEach(request => {
        request.reject(error);
      });
    }
  }
}

Implementation Patterns

Graceful Degradation

Implement fallback mechanisms when certain tools or resources become unavailable.

class ResilientMCPClient {
  private fallbackStrategies: Map<string, FallbackStrategy> = new Map();
  
  async callTool(name: string, args: any): Promise<ToolResult> {
    try {
      return await this.client.callTool(name, args);
    } catch (error) {
      const fallback = this.fallbackStrategies.get(name);
      
      if (fallback) {
        console.warn(`Tool ${name} failed, using fallback strategy`);
        return await fallback.execute(args);
      }
      
      throw error;
    }
  }
  
  registerFallback(toolName: string, strategy: FallbackStrategy): void {
    this.fallbackStrategies.set(toolName, strategy);
  }
}

Health Monitoring

class HealthMonitor {
  private healthChecks: Map<string, HealthCheck> = new Map();
  private metrics: HealthMetrics = new HealthMetrics();
  
  registerHealthCheck(name: string, check: HealthCheck): void {
    this.healthChecks.set(name, check);
  }
  
  async getHealthStatus(): Promise<HealthStatus> {
    const results: HealthCheckResult[] = [];
    
    for (const [name, check] of this.healthChecks) {
      try {
        const startTime = Date.now();
        const result = await Promise.race([
          check.execute(),
          this.timeout(5000)
        ]);
        
        const duration = Date.now() - startTime;
        this.metrics.recordHealthCheck(name, duration, true);
        
        results.push({
          name,
          status: 'healthy',
          duration,
          details: result
        });
      } catch (error) {
        this.metrics.recordHealthCheck(name, 0, false);
        
        results.push({
          name,
          status: 'unhealthy',
          error: error.message
        });
      }
    }
    
    return {
      status: results.every(r => r.status === 'healthy') ? 'healthy' : 'degraded',
      checks: results,
      timestamp: Date.now()
    };
  }
}

Advanced Topics

Custom Transport Implementation

Create specialized transports for unique deployment requirements.

// Redis-based transport for distributed systems
class RedisTransport implements Transport {
  private redis: Redis;
  private responseChannels: Map<string, Promise<MCPResponse>> = new Map();
  
  constructor(redisConfig: RedisConfig) {
    this.redis = new Redis(redisConfig);
    this.setupResponseListener();
  }
  
  async send(message: MCPMessage): Promise<MCPResponse> {
    const messageId = message.id || generateId();
    const responseChannel = `mcp:response:${messageId}`;
    
    // Setup response listener
    const responsePromise = new Promise<MCPResponse>((resolve, reject) => {
      const timeout = setTimeout(() => {
        this.responseChannels.delete(messageId);
        reject(new Error('Request timeout'));
      }, 30000);
      
      this.responseChannels.set(messageId, { resolve, reject, timeout });
    });
    
    // Send request
    await this.redis.lpush('mcp:requests', JSON.stringify({
      ...message,
      id: messageId,
      responseChannel
    }));
    
    return responsePromise;
  }
  
  private setupResponseListener(): void {
    this.redis.subscribe('mcp:responses:*');
    this.redis.on('message', (channel, message) => {
      const messageId = channel.split(':').pop();
      const pendingResponse = this.responseChannels.get(messageId);
      
      if (pendingResponse) {
        clearTimeout(pendingResponse.timeout);
        this.responseChannels.delete(messageId);
        
        try {
          const response = JSON.parse(message);
          pendingResponse.resolve(response);
        } catch (error) {
          pendingResponse.reject(error);
        }
      }
    });
  }
}

Schema Evolution

Handle schema changes gracefully in production environments.

class SchemaVersionManager {
  private migrations: Map<string, SchemaMigration[]> = new Map();
  
  registerMigration(fromVersion: string, toVersion: string, migration: SchemaMigration): void {
    const key = `${fromVersion}->${toVersion}`;
    if (!this.migrations.has(key)) {
      this.migrations.set(key, []);
    }
    this.migrations.get(key)!.push(migration);
  }
  
  async migrateMessage(message: MCPMessage, fromVersion: string, toVersion: string): Promise<MCPMessage> {
    const migrationPath = this.findMigrationPath(fromVersion, toVersion);
    
    let currentMessage = message;
    for (const migration of migrationPath) {
      currentMessage = await migration.apply(currentMessage);
    }
    
    return currentMessage;
  }
  
  private findMigrationPath(from: string, to: string): SchemaMigration[] {
    // Implement path finding algorithm (BFS/DFS)
    // Return sequence of migrations to apply
    return [];
  }
}

Conclusion

MCP's architecture demonstrates thoughtful design that balances simplicity with production requirements. The layered approach, transport agnosticism, and security-first design make it suitable for everything from local development tools to large-scale distributed AI systems.

"Architecture is about the important stuff... whatever that is." - Ralph Johnson. In MCP's case, the "important stuff" is enabling reliable, secure, and scalable AI integration.

The future of AI integration is built on solid architectural foundations. MCP provides those foundations while remaining flexible enough to evolve with the rapidly changing AI landscape.