diff --git a/compiler/src/dotty/tools/backend/jvm/BCodeSkelBuilder.scala b/compiler/src/dotty/tools/backend/jvm/BCodeSkelBuilder.scala
index 394700c2898e..4f4caf36d92a 100644
--- a/compiler/src/dotty/tools/backend/jvm/BCodeSkelBuilder.scala
+++ b/compiler/src/dotty/tools/backend/jvm/BCodeSkelBuilder.scala
@@ -623,7 +623,13 @@ trait BCodeSkelBuilder extends BCodeHelpers {
       }
 
       if (emitLines && tree.span.exists && !tree.hasAttachment(SyntheticUnit)) {
-        val nr = ctx.source.offsetToLine(tree.span.point) + 1
+        val nr =
+          val sourcePos = tree.sourcePos
+          (
+            if sourcePos.exists then sourcePos.source.positionInUltimateSource(sourcePos).line
+            else ctx.source.offsetToLine(tree.span.point) // fallback
+          ) + 1
+
         if (nr != lastEmittedLineNr) {
           lastEmittedLineNr = nr
           getNonLabelNode(lastInsn) match {
diff --git a/compiler/src/dotty/tools/dotc/util/SourceFile.scala b/compiler/src/dotty/tools/dotc/util/SourceFile.scala
index 9da4f58f2deb..3ea43d16a7c8 100644
--- a/compiler/src/dotty/tools/dotc/util/SourceFile.scala
+++ b/compiler/src/dotty/tools/dotc/util/SourceFile.scala
@@ -119,7 +119,8 @@ class SourceFile(val file: AbstractFile, computeContent: => Array[Char]) extends
    *  For regular source files, simply return the argument.
    */
   def positionInUltimateSource(position: SourcePosition): SourcePosition =
-    SourcePosition(underlying, position.span shift start)
+    if isSelfContained then position // return the argument
+    else SourcePosition(underlying, position.span shift start)
 
   private def calculateLineIndicesFromContents() = {
     val cs = content()
diff --git a/compiler/src/dotty/tools/dotc/util/SourcePosition.scala b/compiler/src/dotty/tools/dotc/util/SourcePosition.scala
index 904704b2349c..a7358755043c 100644
--- a/compiler/src/dotty/tools/dotc/util/SourcePosition.scala
+++ b/compiler/src/dotty/tools/dotc/util/SourcePosition.scala
@@ -79,7 +79,6 @@ extends SrcPos, interfaces.SourcePosition, Showable {
     rec(this)
   }
 
-
   override def toString: String =
     s"${if (source.exists) source.file.toString else "(no source)"}:$span"
 
diff --git a/compiler/test/dotty/tools/dotc/BootstrappedOnlyCompilationTests.scala b/compiler/test/dotty/tools/dotc/BootstrappedOnlyCompilationTests.scala
index a40c1ec1e5b2..5cd4f837b823 100644
--- a/compiler/test/dotty/tools/dotc/BootstrappedOnlyCompilationTests.scala
+++ b/compiler/test/dotty/tools/dotc/BootstrappedOnlyCompilationTests.scala
@@ -193,7 +193,7 @@ class BootstrappedOnlyCompilationTests {
 
     // 1. hack with absolute path for -Xplugin
     // 2. copy `pluginFile` to destination
-    def compileFilesInDir(dir: String): CompilationTest = {
+    def compileFilesInDir(dir: String, run: Boolean = false): CompilationTest = {
       val outDir = defaultOutputDir + "testPlugins/"
       val sourceDir = new java.io.File(dir)
 
@@ -201,7 +201,10 @@ class BootstrappedOnlyCompilationTests {
       val targets = dirs.map { dir =>
         val compileDir = createOutputDirsForDir(dir, sourceDir, outDir)
         Files.copy(dir.toPath.resolve(pluginFile), compileDir.toPath.resolve(pluginFile), StandardCopyOption.REPLACE_EXISTING)
-        val flags = TestFlags(withCompilerClasspath, noCheckOptions).and("-Xplugin:" + compileDir.getAbsolutePath)
+        val flags = {
+          val base = TestFlags(withCompilerClasspath, noCheckOptions).and("-Xplugin:" + compileDir.getAbsolutePath)
+          if run then base.withRunClasspath(withCompilerClasspath) else base
+        }
         SeparateCompilationSource("testPlugins", dir, flags, compileDir)
       }
 
@@ -210,6 +213,7 @@ class BootstrappedOnlyCompilationTests {
 
     compileFilesInDir("tests/plugins/neg").checkExpectedErrors()
     compileDir("tests/plugins/custom/analyzer", withCompilerOptions.and("-Yretain-trees")).checkCompile()
+    compileFilesInDir("tests/plugins/run", run = true).checkRuns()
   }
 }
 
diff --git a/tests/plugins/run/scriptWrapper/Framework_1.scala b/tests/plugins/run/scriptWrapper/Framework_1.scala
new file mode 100644
index 000000000000..c8a15de8342b
--- /dev/null
+++ b/tests/plugins/run/scriptWrapper/Framework_1.scala
@@ -0,0 +1,3 @@
+package framework
+
+class entrypoint extends scala.annotation.Annotation
diff --git a/tests/plugins/run/scriptWrapper/LineNumberPlugin_1.scala b/tests/plugins/run/scriptWrapper/LineNumberPlugin_1.scala
new file mode 100644
index 000000000000..888d5f95838d
--- /dev/null
+++ b/tests/plugins/run/scriptWrapper/LineNumberPlugin_1.scala
@@ -0,0 +1,68 @@
+package scriptWrapper
+
+import dotty.tools.dotc.*
+import core.*
+import Contexts.Context
+import Contexts.ctx
+import plugins.*
+import ast.tpd
+import util.SourceFile
+
+class LineNumberPlugin extends StandardPlugin {
+  val name: String = "linenumbers"
+  val description: String = "adjusts line numbers of script files"
+
+  override def initialize(options: List[String])(using Context): List[PluginPhase] = FixLineNumbers() :: Nil
+}
+
+// Loosely follows Mill linenumbers plugin (scan for marker with "original" source, adjust line numbers to match)
+class FixLineNumbers extends PluginPhase {
+
+  val codeMarker = "//USER_CODE_HERE"
+
+  def phaseName: String = "fixLineNumbers"
+  override def runsAfter: Set[String] = Set("posttyper")
+  override def runsBefore: Set[String] = Set("pickler")
+
+  override def transformUnit(tree: tpd.Tree)(using Context): tpd.Tree = {
+    val sourceContent = ctx.source.content()
+    val lines = new String(sourceContent).linesWithSeparators.toVector
+    val codeMarkerLine = lines.indexWhere(_.startsWith(codeMarker))
+
+    if codeMarkerLine < 0 then
+      tree
+    else
+      val adjustedFile = lines.collectFirst {
+        case s"//USER_SRC_FILE:./$file" => file.trim
+      }.getOrElse("<unknown>")
+
+      val adjustedSrc = ctx.source.file.container.lookupName(adjustedFile, directory = false) match
+        case null =>
+          report.error(s"could not find file $adjustedFile", tree.sourcePos)
+          return tree
+        case file =>
+          SourceFile(file, scala.io.Codec.UTF8)
+
+      val userCodeOffset = ctx.source.lineToOffset(codeMarkerLine + 1) // lines.take(codeMarkerLine).map(_.length).sum
+      val lineMapper = LineMapper(codeMarkerLine, userCodeOffset, adjustedSrc)
+      lineMapper.transform(tree)
+  }
+
+}
+
+class LineMapper(markerLine: Int, userCodeOffset: Int, adjustedSrc: SourceFile) extends tpd.TreeMapWithPreciseStatContexts() {
+
+  override def transform(tree: tpd.Tree)(using Context): tpd.Tree = {
+    val tree0 = super.transform(tree)
+    val pos = tree0.sourcePos
+    if pos.exists && pos.start >= userCodeOffset then
+      val tree1 = tree0.cloneIn(adjustedSrc).withSpan(pos.span.shift(-userCodeOffset))
+      // if tree1.show.toString == "???" then
+      //   val pos1 = tree1.sourcePos
+      //   sys.error(s"rewrote ??? at ${pos1.source}:${pos1.line + 1}:${pos1.column + 1} (sourced from ${markerLine + 2})")
+      tree1
+    else
+      tree0
+  }
+
+}
diff --git a/tests/plugins/run/scriptWrapper/Test_3.scala b/tests/plugins/run/scriptWrapper/Test_3.scala
new file mode 100644
index 000000000000..341af27ee433
--- /dev/null
+++ b/tests/plugins/run/scriptWrapper/Test_3.scala
@@ -0,0 +1,25 @@
+@main def Test: Unit = {
+  val mainCls = Class.forName("foo_sc")
+  val mainMethod = mainCls.getMethod("main", classOf[Array[String]])
+  val stackTrace: Array[String] = {
+    try
+      mainMethod.invoke(null, Array.empty[String])
+      sys.error("Expected an exception")
+    catch
+      case e: java.lang.reflect.InvocationTargetException =>
+        val cause = e.getCause
+        if cause != null then
+          cause.getStackTrace.map(_.toString)
+        else
+          throw e
+  }
+
+  val expected = Set(
+    "foo_sc$.getRandom(foo_2.scala:3)", // adjusted line number (11 -> 3)
+    "foo_sc$.brokenRandom(foo_2.scala:5)", // adjusted line number (13 -> 5)
+    "foo_sc$.run(foo_2.scala:8)", // adjusted line number (16 -> 8)
+  )
+
+  val missing = expected -- stackTrace
+  assert(missing.isEmpty, s"Missing: $missing")
+}
diff --git a/tests/plugins/run/scriptWrapper/foo_2.scala b/tests/plugins/run/scriptWrapper/foo_2.scala
new file mode 100644
index 000000000000..02e3f034e757
--- /dev/null
+++ b/tests/plugins/run/scriptWrapper/foo_2.scala
@@ -0,0 +1,18 @@
+// generated code
+// script: foo.sc
+object foo_sc {
+def main(args: Array[String]): Unit = {
+  run // assume some macro generates this by scanning for @entrypoint
+}
+//USER_SRC_FILE:./foo_original_2.scala
+//USER_CODE_HERE
+import framework.*
+
+def getRandom: Int = brokenRandom // LINE 3;
+
+def brokenRandom: Int = ??? // LINE 5;
+
+@entrypoint
+def run = println("Hello, here is a random number: " + getRandom) // LINE 8;
+//END_USER_CODE_HERE
+}
diff --git a/tests/plugins/run/scriptWrapper/foo_original_2.scala b/tests/plugins/run/scriptWrapper/foo_original_2.scala
new file mode 100644
index 000000000000..162ddd1724a1
--- /dev/null
+++ b/tests/plugins/run/scriptWrapper/foo_original_2.scala
@@ -0,0 +1,8 @@
+import framework.*
+
+def getRandom: Int = brokenRandom // LINE 3;
+
+def brokenRandom: Int = ??? // LINE 5;
+
+@entrypoint
+def run = println("Hello, here is a random number: " + getRandom) // LINE 8;
diff --git a/tests/plugins/run/scriptWrapper/plugin.properties b/tests/plugins/run/scriptWrapper/plugin.properties
new file mode 100644
index 000000000000..f1fc6067e611
--- /dev/null
+++ b/tests/plugins/run/scriptWrapper/plugin.properties
@@ -0,0 +1 @@
+pluginClass=scriptWrapper.LineNumberPlugin