diff --git a/src/lib/application.ts b/src/lib/application.ts
index 3d063b250..122c5367f 100644
--- a/src/lib/application.ts
+++ b/src/lib/application.ts
@@ -115,7 +115,7 @@ export class Application extends ChildableComponent<Application, AbstractCompone
         }
 
         this.plugins.load();
-        return this.options.read(options, OptionsReadMode.Fetch);
+        return this.options.read(this.options.getRawValues(), OptionsReadMode.Fetch);
     }
 
     /**
diff --git a/src/lib/utils/options/readers/arguments.ts b/src/lib/utils/options/readers/arguments.ts
index d6c4c7c64..d904a2d7d 100644
--- a/src/lib/utils/options/readers/arguments.ts
+++ b/src/lib/utils/options/readers/arguments.ts
@@ -58,7 +58,7 @@ export class ArgumentsReader extends OptionsComponent {
                 files.push(arg);
             }
         }
-        if (files) {
+        if (files && files.length > 0) {
             event.inputFiles = files;
         }
     }
diff --git a/src/lib/utils/options/readers/tsconfig.ts b/src/lib/utils/options/readers/tsconfig.ts
index f1aef133b..d0430bb9e 100644
--- a/src/lib/utils/options/readers/tsconfig.ts
+++ b/src/lib/utils/options/readers/tsconfig.ts
@@ -4,7 +4,7 @@ import * as _ from 'lodash';
 import * as ts from 'typescript';
 
 import { Component, Option } from '../../component';
-import { OptionsComponent, DiscoverEvent } from '../options';
+import { OptionsComponent, OptionsReadMode, DiscoverEvent } from '../options';
 import { ParameterType, ParameterHint } from '../declaration';
 import { TypeScriptSource } from '../sources/typescript';
 
@@ -35,6 +35,11 @@ export class TSConfigReader extends OptionsComponent {
     }
 
     onDiscover(event: DiscoverEvent) {
+        // Do nothing until were fetching options
+        if (event.mode !== OptionsReadMode.Fetch) {
+            return;
+        }
+
         if (TSConfigReader.OPTIONS_KEY in event.data) {
             this.load(event, Path.resolve(event.data[TSConfigReader.OPTIONS_KEY]));
         } else if (TSConfigReader.PROJECT_KEY in event.data) {
diff --git a/src/lib/utils/options/readers/typedoc.ts b/src/lib/utils/options/readers/typedoc.ts
index ad5a44f04..a03e8df11 100644
--- a/src/lib/utils/options/readers/typedoc.ts
+++ b/src/lib/utils/options/readers/typedoc.ts
@@ -3,7 +3,7 @@ import * as FS from 'fs';
 import * as _ from 'lodash';
 
 import { Component, Option } from '../../component';
-import { OptionsComponent, DiscoverEvent } from '../options';
+import { OptionsComponent, OptionsReadMode, DiscoverEvent } from '../options';
 import { ParameterType, ParameterHint } from '../declaration';
 
 @Component({name: 'options:typedoc'})
@@ -26,6 +26,11 @@ export class TypedocReader extends OptionsComponent {
     }
 
     onDiscover(event: DiscoverEvent) {
+        // Do nothing until were fetching options
+        if (event.mode !== OptionsReadMode.Fetch) {
+            return;
+        }
+
         if (TypedocReader.OPTIONS_KEY in event.data) {
             this.load(event, Path.resolve(event.data[TypedocReader.OPTIONS_KEY]));
         } else if (this.application.isCLI) {