Version: 5.4 beta (switch to 5.3)
Protecting Content
AssetBundles FAQ

Including scripts in AssetBundles

AssetBundles can contain scripts as TextAssets but as such they will not be actual executable code. If you want to include code in your AssetBundles that can be executed in your application it needs to be pre-compiled into an assembly and loaded using the Mono Reflection class (Note: Reflection is not available on platforms that use AOT compilation, such as iOS). You can create your assemblies in any normal C# IDE (e.g. Monodevelop, Visual Studio) or any text editor using the mono/.net compilers.

Note: Loading scripts from asset bundles is not supported on Windows Store Apps and Windows Phone.

//c# example
string url = "http://www.mywebsite.com/mygame/assetbundles/assetbundle1.unity3d";
IEnumerator Start () {
    while (!Caching.ready)
        yield return null;

    // Start a download of the given URL
    WWW www = WWW.LoadFromCacheOrDownload (url, 1);

    // Wait for download to complete
    yield return www;

    // Load and retrieve the AssetBundle
    AssetBundle bundle = www.assetBundle;

    // Load the TextAsset object
    TextAsset txt = bundle.Load("myBinaryAsText", typeof(TextAsset)) as TextAsset;

    // Load the assembly and get a type (class) from it
    var assembly = System.Reflection.Assembly.Load(txt.bytes);
    var type = assembly.GetType("MyClassDerivedFromMonoBehaviour");

    // Instantiate a GameObject and add a component with the loaded class
    GameObject go = new GameObject();
    go.AddComponent(type);
}

Protecting Content
AssetBundles FAQ