diff --git a/src/main/java/org/scijava/script/ScriptFinder.java b/src/main/java/org/scijava/script/ScriptFinder.java
index ea438791e..23701ea99 100644
--- a/src/main/java/org/scijava/script/ScriptFinder.java
+++ b/src/main/java/org/scijava/script/ScriptFinder.java
@@ -41,6 +41,7 @@
 
 import org.scijava.AbstractContextual;
 import org.scijava.Context;
+import org.scijava.MenuEntry;
 import org.scijava.MenuPath;
 import org.scijava.log.LogService;
 import org.scijava.plugin.Parameter;
@@ -178,8 +179,11 @@ private int createInfos(final List<ScriptInfo> scripts, final Set<URL> urls,
 			// friendlyPath = "File/Import/Movie File..."
 			// menuPath = File > Import > Movie File...
 
-			// NB: Ignore base-level scripts (not nested in any menu).
-			if (menuPath.size() == 1) continue;
+			// Place base-level scripts in the "Plugins>Scripts" submenu
+			if (menuPath.size() == 1){
+				menuPath.add(0, new MenuEntry("Plugins"));
+				menuPath.add(1, new MenuEntry("Scripts"));
+			}
 
 			final URL url = scriptMap.get(path);
 
diff --git a/src/test/java/org/scijava/script/ScriptFinderTest.java b/src/test/java/org/scijava/script/ScriptFinderTest.java
index f3301fec1..e28869372 100644
--- a/src/test/java/org/scijava/script/ScriptFinderTest.java
+++ b/src/test/java/org/scijava/script/ScriptFinderTest.java
@@ -66,7 +66,7 @@ public class ScriptFinderTest {
 	public static void setUp() throws IOException {
 		scriptsDir = TestUtils.createTemporaryDirectory("script-finder-");
 		final String[] scriptPaths = { //
-			"ignored.foo", //
+			"script_in_base_dir.foo", //
 			"Scripts/quick.foo", //
 			"Scripts/brown.foo", //
 			"Scripts/fox.foo", //
@@ -108,6 +108,7 @@ public void testFindScripts() {
 			"Math > multiply", //
 			"Math > pow", //
 			"Scripts > quick", //
+			"Plugins > Scripts > script in base dir", //
 			"Math > Trig > sin", //
 			"Math > subtract", //
 			"Math > Trig > tan", //
@@ -139,10 +140,10 @@ public void testMenuPrefixes() {
 			"Foo > Bar > Math > Trig > cos", //
 			"Foo > Bar > Math > divide", //
 			"Foo > Bar > Scripts > fox", //
-			"Foo > Bar > ignored", //
 			"Foo > Bar > Math > multiply", //
 			"Math > pow", //
 			"Foo > Bar > Scripts > quick", //
+			"Foo > Bar > script in base dir", //
 			"Foo > Bar > Math > Trig > sin", //
 			"Foo > Bar > Math > subtract", //
 			"Foo > Bar > Math > Trig > tan", //
@@ -177,6 +178,7 @@ public void testOverlappingDirectories() {
 			"Math > multiply", //
 			"Math > pow", //
 			"Plugins > quick", //
+			"Plugins > Scripts > script in base dir", //
 			"Math > Trig > sin", //
 			"Math > subtract", //
 			"Math > Trig > tan", //