diff --git a/flake8/checker.py b/flake8/checker.py
index c449a9b..905cade 100644
--- a/flake8/checker.py
+++ b/flake8/checker.py
@@ -326,6 +326,37 @@ class FileChecker(object):
         self.processor.keyword_arguments_for(plugin.parameters, arguments)
         return plugin.execute(**arguments)
 
+    def run_ast_checks(self):
+        """Run all checks expecting an abstract syntax tree."""
+        try:
+            ast = self.processor.build_ast()
+        except (ValueError, SyntaxError, TypeError):
+            (exc_type, exception) = sys.exc_info()[:2]
+            if len(exception.args) > 1:
+                offset = exception.args[1]
+                if len(offset) > 2:
+                    offset = offset[1:3]
+            else:
+                offset = (1, 0)
+
+            self.report('E999', offset[0], offset[1], '%s: %s' %
+                        (exc_type.__name__, exception.args[0]))
+            return
+
+        for plugin in self.checks.ast_plugins:
+            checker = self.run_check(plugin, tree=ast)
+            # NOTE(sigmavirus24): If we want to allow for AST plugins that are
+            # not classes exclusively, we can do the following:
+            # retrieve_results = getattr(checker, 'run', lambda: checker)
+            # Otherwise, we just call run on the checker
+            for (line_number, offset, text, check) in checker.run():
+                self.report(
+                    error_code=None,
+                    line_number=line_number,
+                    column=offset,
+                    text=text,
+                )
+
     def run_logical_checks(self):
         """Run all checks expecting a logical line."""
         comments, logical_line, mapping = self.processor.build_logical_line()
@@ -404,6 +435,8 @@ class FileChecker(object):
             self.report(exc.error_code, exc.line_number, exc.column_number,
                         exc.error_message)
 
+        self.run_ast_checks()
+
         if results_queue is not None:
             results_queue.put((self.filename, self.results))
 
diff --git a/flake8/main/cli.py b/flake8/main/cli.py
index 5bf6144..dbd9603 100644
--- a/flake8/main/cli.py
+++ b/flake8/main/cli.py
@@ -227,6 +227,9 @@ class Application(object):
                 self.option_manager, argv
             )
 
+        self.check_plugins.provide_options(self.option_manager, self.options,
+                                           self.args)
+
     def make_formatter(self):
         # type: () -> NoneType
         """Initialize a formatter based on the parsed options."""
diff --git a/flake8/processor.py b/flake8/processor.py
index d75256b..1dc27a1 100644
--- a/flake8/processor.py
+++ b/flake8/processor.py
@@ -10,6 +10,7 @@ from flake8 import defaults
 from flake8 import exceptions
 from flake8 import utils
 
+PyCF_ONLY_AST = 1024
 NEWLINE = frozenset([tokenize.NL, tokenize.NEWLINE])
 # Work around Python < 2.6 behaviour, which does not generate NL after
 # a comment which is on a line by itself.
@@ -172,6 +173,10 @@ class FileProcessor(object):
             (previous_row, previous_column) = end
         return comments, logical, mapping
 
+    def build_ast(self):
+        """Build an abstract syntax tree from the list of lines."""
+        return compile(''.join(self.lines), '', 'exec', PyCF_ONLY_AST)
+
     def build_logical_line(self):
         """Build a logical line from the current tokens list."""
         comments, logical, mapping_list = self.build_logical_line_tokens()
@@ -223,6 +228,10 @@ class FileProcessor(object):
         except tokenize.TokenError as exc:
             raise exceptions.InvalidSyntax(exc.message, exception=exc)
 
+    def line_for(self, line_number):
+        """Retrieve the physical line at the specified line number."""
+        return self.lines[line_number - 1]
+
     def next_line(self):
         """Get the next line from the list."""
         if self.line_number >= self.total_lines:
diff --git a/flake8/style_guide.py b/flake8/style_guide.py
index 51c3a8e..2c18c9d 100644
--- a/flake8/style_guide.py
+++ b/flake8/style_guide.py
@@ -187,12 +187,13 @@ class StyleGuide(object):
                   error, codes_str)
         return False
 
-    def handle_error(self, code, filename, line_number, column_number, text):
+    def handle_error(self, code, filename, line_number, column_number, text,
+                     physical_line=None):
         # type: (str, str, int, int, str) -> NoneType
         """Handle an error reported by a check."""
         error = Error(code, filename, line_number, column_number, text)
         if (self.should_report_error(error.code) is Decision.Selected and
-                self.is_inline_ignored(error) is False):
+                self.is_inline_ignored(error, physical_line) is False):
             self.formatter.handle(error)
             self.listener.notify(error.code, error)