Can I handle alert inside UIWebViewDelegate?

A better solution to this problem is to create a Category for UIWebView for the method

webView:runJavaScriptAlertPanelWithMessage:initiatedByFrame:

So that you can handle the alert event in any way that you'd like. I did this because I don't like the default behavior of UIWebView when it puts the filename of the source in the UIAlertView title. The Category looks something like this,

@interface UIWebView (JavaScriptAlert) 

- (void)webView:(UIWebView *)sender runJavaScriptAlertPanelWithMessage:(NSString *)message initiatedByFrame:(WebFrame *)frame;

@end

@implementation UIWebView (JavaScriptAlert)

- (void)webView:(UIWebView *)sender runJavaScriptAlertPanelWithMessage:(NSString *)message initiatedByFrame:(WebFrame *)frame {
    UIAlertView* dialogue = [[UIAlertView alloc] initWithTitle:nil message:message delegate:nil cancelButtonTitle:@"Okay" otherButtonTitles:nil];
    [dialogue show];
    [dialogue autorelease];
}

@end

This seems to do it:

- (void)webViewDidFinishLoad:(UIWebView *)webView
{
    JSContext *ctx = [webView valueForKeyPath:@"documentView.webView.mainFrame.javaScriptContext"];
    ctx[@"window"][@"alert"] = ^(JSValue *message) {
        UIAlertView *alert = [[UIAlertView alloc] initWithTitle:@"JavaScript Alert" message:[message toString] delegate:nil cancelButtonTitle:@"OK" otherButtonTitles:nil];
        [alert show];
    };
}

Note: only tested on iOS 8.

If by "contain a flash" you mean the page you're loading into your web view has an Adobe Flash movie in it, you're out of luck, I'm afraid. Mobile Safari doesn't support Flash, and most likely never will.

In the general case, if you want JavaScript running in a web view to communicate with the native app hosting it, you can load fake URLs (for example: "myapp://alert?The+text+of+the+alert+goes+here."). That will trigger the webView:shouldStartLoadWithRequest:navigationType: delegate method. In that method, inspect the request, and if the URL being loaded is one of these internal communications, trigger the appropriate action in your app, and return NO.