diff --git a/sql/catalyst/src/main/scala/org/apache/spark/sql/catalyst/trees/TreeNode.scala b/sql/catalyst/src/main/scala/org/apache/spark/sql/catalyst/trees/TreeNode.scala
index 0596dc00985a..e79000d58350 100644
--- a/sql/catalyst/src/main/scala/org/apache/spark/sql/catalyst/trees/TreeNode.scala
+++ b/sql/catalyst/src/main/scala/org/apache/spark/sql/catalyst/trees/TreeNode.scala
@@ -287,7 +287,7 @@ abstract class TreeNode[BaseType <: TreeNode[BaseType]] extends Product {
       mapChildren(_.transformDown(rule))
     } else {
       // If the transform function replaces this node with a new one, carry over the tags.
-      afterRule.tags ++= this.tags
+      afterRule.copyTagsFrom(this)
       afterRule.mapChildren(_.transformDown(rule))
     }
   }
@@ -311,7 +311,7 @@ abstract class TreeNode[BaseType <: TreeNode[BaseType]] extends Product {
       }
     }
     // If the transform function replaces this node with a new one, carry over the tags.
-    newNode.tags ++= this.tags
+    newNode.copyTagsFrom(this)
     newNode
   }
 
@@ -429,8 +429,15 @@ abstract class TreeNode[BaseType <: TreeNode[BaseType]] extends Product {
   private def makeCopy(
       newArgs: Array[AnyRef],
       allowEmptyArgs: Boolean): BaseType = attachTree(this, "makeCopy") {
+    val allCtors = getClass.getConstructors
+    if (newArgs.isEmpty && allCtors.isEmpty) {
+      // This is a singleton object which doesn't have any constructor. Just return `this` as we
+      // can't copy it.
+      return this
+    }
+
     // Skip no-arg constructors that are just there for kryo.
-    val ctors = getClass.getConstructors.filter(allowEmptyArgs || _.getParameterTypes.size != 0)
+    val ctors = allCtors.filter(allowEmptyArgs || _.getParameterTypes.size != 0)
     if (ctors.isEmpty) {
       sys.error(s"No valid constructor for $nodeName")
     }
diff --git a/sql/core/src/main/scala/org/apache/spark/sql/execution/QueryExecution.scala b/sql/core/src/main/scala/org/apache/spark/sql/execution/QueryExecution.scala
index c8531e9a046a..1583b8d3a1f9 100644
--- a/sql/core/src/main/scala/org/apache/spark/sql/execution/QueryExecution.scala
+++ b/sql/core/src/main/scala/org/apache/spark/sql/execution/QueryExecution.scala
@@ -28,7 +28,7 @@ import org.apache.spark.sql.catalyst.analysis.UnsupportedOperationChecker
 import org.apache.spark.sql.catalyst.plans.QueryPlan
 import org.apache.spark.sql.catalyst.plans.logical.{LogicalPlan, ReturnAnswer}
 import org.apache.spark.sql.catalyst.rules.Rule
-import org.apache.spark.sql.catalyst.util.StringUtils.{PlanStringConcat, StringConcat}
+import org.apache.spark.sql.catalyst.util.StringUtils.PlanStringConcat
 import org.apache.spark.sql.catalyst.util.truncatedString
 import org.apache.spark.sql.execution.adaptive.InsertAdaptiveSparkPlan
 import org.apache.spark.sql.execution.exchange.{EnsureRequirements, ReuseExchange}
@@ -60,36 +60,38 @@ class QueryExecution(
 
   lazy val analyzed: LogicalPlan = tracker.measurePhase(QueryPlanningTracker.ANALYSIS) {
     SparkSession.setActiveSession(sparkSession)
+    // We can't clone `logical` here, which will reset the `_analyzed` flag.
     sparkSession.sessionState.analyzer.executeAndCheck(logical, tracker)
   }
 
   lazy val withCachedData: LogicalPlan = {
     assertAnalyzed()
     assertSupported()
-    sparkSession.sharedState.cacheManager.useCachedData(analyzed)
+    // clone the plan to avoid sharing the plan instance between different stages like analyzing,
+    // optimizing and planning.
+    sparkSession.sharedState.cacheManager.useCachedData(analyzed.clone())
   }
 
   lazy val optimizedPlan: LogicalPlan = tracker.measurePhase(QueryPlanningTracker.OPTIMIZATION) {
-    sparkSession.sessionState.optimizer.executeAndTrack(withCachedData, tracker)
+    // clone the plan to avoid sharing the plan instance between different stages like analyzing,
+    // optimizing and planning.
+    sparkSession.sessionState.optimizer.executeAndTrack(withCachedData.clone(), tracker)
   }
 
   lazy val sparkPlan: SparkPlan = tracker.measurePhase(QueryPlanningTracker.PLANNING) {
     SparkSession.setActiveSession(sparkSession)
-    // Runtime re-optimization requires a unique instance of every node in the logical plan.
-    val logicalPlan = if (sparkSession.sessionState.conf.adaptiveExecutionEnabled) {
-      optimizedPlan.clone()
-    } else {
-      optimizedPlan
-    }
     // TODO: We use next(), i.e. take the first plan returned by the planner, here for now,
     //       but we will implement to choose the best plan.
-    planner.plan(ReturnAnswer(logicalPlan)).next()
+    // Clone the logical plan here, in case the planner rules change the states of the logical plan.
+    planner.plan(ReturnAnswer(optimizedPlan.clone())).next()
   }
 
   // executedPlan should not be used to initialize any SparkPlan. It should be
   // only used for execution.
   lazy val executedPlan: SparkPlan = tracker.measurePhase(QueryPlanningTracker.PLANNING) {
-    prepareForExecution(sparkPlan)
+    // clone the plan to avoid sharing the plan instance between different stages like analyzing,
+    // optimizing and planning.
+    prepareForExecution(sparkPlan.clone())
   }
 
   /**
diff --git a/sql/core/src/main/scala/org/apache/spark/sql/execution/columnar/InMemoryRelation.scala b/sql/core/src/main/scala/org/apache/spark/sql/execution/columnar/InMemoryRelation.scala
index 1de2b6e0a85d..b77f90d19b62 100644
--- a/sql/core/src/main/scala/org/apache/spark/sql/execution/columnar/InMemoryRelation.scala
+++ b/sql/core/src/main/scala/org/apache/spark/sql/execution/columnar/InMemoryRelation.scala
@@ -223,6 +223,13 @@ case class InMemoryRelation(
       statsOfPlanToCache).asInstanceOf[this.type]
   }
 
+  // override `clone` since the default implementation won't carry over mutable states.
+  override def clone(): LogicalPlan = {
+    val cloned = this.copy()
+    cloned.statsOfPlanToCache = this.statsOfPlanToCache
+    cloned
+  }
+
   override def simpleString(maxFields: Int): String =
     s"InMemoryRelation [${truncatedString(output, ", ", maxFields)}], ${cacheBuilder.storageLevel}"
 }
diff --git a/sql/core/src/main/scala/org/apache/spark/sql/execution/command/SetCommand.scala b/sql/core/src/main/scala/org/apache/spark/sql/execution/command/SetCommand.scala
index 45c62b467657..39b08e2894dc 100644
--- a/sql/core/src/main/scala/org/apache/spark/sql/execution/command/SetCommand.scala
+++ b/sql/core/src/main/scala/org/apache/spark/sql/execution/command/SetCommand.scala
@@ -20,7 +20,7 @@ package org.apache.spark.sql.execution.command
 import org.apache.spark.internal.Logging
 import org.apache.spark.sql.{Row, SparkSession}
 import org.apache.spark.sql.catalyst.expressions.Attribute
-import org.apache.spark.sql.catalyst.plans.logical.IgnoreCachedData
+import org.apache.spark.sql.catalyst.plans.logical.{IgnoreCachedData, LogicalPlan}
 import org.apache.spark.sql.internal.SQLConf
 import org.apache.spark.sql.internal.StaticSQLConf.CATALOG_IMPLEMENTATION
 import org.apache.spark.sql.types.{StringType, StructField, StructType}
diff --git a/sql/core/src/main/scala/org/apache/spark/sql/execution/datasources/SaveIntoDataSourceCommand.scala b/sql/core/src/main/scala/org/apache/spark/sql/execution/datasources/SaveIntoDataSourceCommand.scala
index f29e7869fb27..a1de287b93f9 100644
--- a/sql/core/src/main/scala/org/apache/spark/sql/execution/datasources/SaveIntoDataSourceCommand.scala
+++ b/sql/core/src/main/scala/org/apache/spark/sql/execution/datasources/SaveIntoDataSourceCommand.scala
@@ -52,4 +52,10 @@ case class SaveIntoDataSourceCommand(
     val redacted = SQLConf.get.redactOptions(options)
     s"SaveIntoDataSourceCommand ${dataSource}, ${redacted}, ${mode}"
   }
+
+  // Override `clone` since the default implementation will turn `CaseInsensitiveMap` to a normal
+  // map.
+  override def clone(): LogicalPlan = {
+    SaveIntoDataSourceCommand(query.clone(), dataSource, options, mode)
+  }
 }
diff --git a/sql/core/src/test/scala/org/apache/spark/sql/execution/QueryExecutionSuite.scala b/sql/core/src/test/scala/org/apache/spark/sql/execution/QueryExecutionSuite.scala
index 7de5e826f667..39c87c9eeb47 100644
--- a/sql/core/src/test/scala/org/apache/spark/sql/execution/QueryExecutionSuite.scala
+++ b/sql/core/src/test/scala/org/apache/spark/sql/execution/QueryExecutionSuite.scala
@@ -18,8 +18,10 @@ package org.apache.spark.sql.execution
 
 import scala.io.Source
 
-import org.apache.spark.sql.AnalysisException
+import org.apache.spark.sql.{AnalysisException, FastOperator}
+import org.apache.spark.sql.catalyst.plans.QueryPlan
 import org.apache.spark.sql.catalyst.plans.logical.{LogicalPlan, OneRowRelation}
+import org.apache.spark.sql.catalyst.trees.TreeNodeTag
 import org.apache.spark.sql.internal.SQLConf
 import org.apache.spark.sql.test.SharedSQLContext
 
@@ -137,5 +139,56 @@ class QueryExecutionSuite extends SharedSQLContext {
       (_: LogicalPlan) => throw new Error("error"))
     val error = intercept[Error](qe.toString)
     assert(error.getMessage.contains("error"))
+
+    spark.experimental.extraStrategies = Nil
+  }
+
+  test("SPARK-28346: clone the query plan between different stages") {
+    val tag1 = new TreeNodeTag[String]("a")
+    val tag2 = new TreeNodeTag[String]("b")
+    val tag3 = new TreeNodeTag[String]("c")
+
+    def assertNoTag(tag: TreeNodeTag[String], plans: QueryPlan[_]*): Unit = {
+      plans.foreach { plan =>
+        assert(plan.getTagValue(tag).isEmpty)
+      }
+    }
+
+    val df = spark.range(10)
+    val analyzedPlan = df.queryExecution.analyzed
+    val cachedPlan = df.queryExecution.withCachedData
+    val optimizedPlan = df.queryExecution.optimizedPlan
+
+    analyzedPlan.setTagValue(tag1, "v")
+    assertNoTag(tag1, cachedPlan, optimizedPlan)
+
+    cachedPlan.setTagValue(tag2, "v")
+    assertNoTag(tag2, analyzedPlan, optimizedPlan)
+
+    optimizedPlan.setTagValue(tag3, "v")
+    assertNoTag(tag3, analyzedPlan, cachedPlan)
+
+    val tag4 = new TreeNodeTag[String]("d")
+    try {
+      spark.experimental.extraStrategies = Seq(new SparkStrategy() {
+        override def apply(plan: LogicalPlan): Seq[SparkPlan] = {
+          plan.foreach {
+            case r: org.apache.spark.sql.catalyst.plans.logical.Range =>
+              r.setTagValue(tag4, "v")
+            case _ =>
+          }
+          Seq(FastOperator(plan.output))
+        }
+      })
+      // trigger planning
+      df.queryExecution.sparkPlan
+      assert(optimizedPlan.getTagValue(tag4).isEmpty)
+    } finally {
+      spark.experimental.extraStrategies = Nil
+    }
+
+    val tag5 = new TreeNodeTag[String]("e")
+    df.queryExecution.executedPlan.setTagValue(tag5, "v")
+    assertNoTag(tag5, df.queryExecution.sparkPlan)
   }
 }
diff --git a/sql/core/src/test/scala/org/apache/spark/sql/execution/columnar/PartitionBatchPruningSuite.scala b/sql/core/src/test/scala/org/apache/spark/sql/execution/columnar/PartitionBatchPruningSuite.scala
index b3a5c687f775..b4c1472ecb81 100644
--- a/sql/core/src/test/scala/org/apache/spark/sql/execution/columnar/PartitionBatchPruningSuite.scala
+++ b/sql/core/src/test/scala/org/apache/spark/sql/execution/columnar/PartitionBatchPruningSuite.scala
@@ -187,7 +187,7 @@ class PartitionBatchPruningSuite
     val result = df.collect().map(_(0)).toArray
     assert(result.length === 1)
 
-    val (readPartitions, readBatches) = df.queryExecution.sparkPlan.collect {
+    val (readPartitions, readBatches) = df.queryExecution.executedPlan.collect {
         case in: InMemoryTableScanExec => (in.readPartitions.value, in.readBatches.value)
       }.head
     assert(readPartitions === 5)
@@ -208,7 +208,7 @@ class PartitionBatchPruningSuite
         df.collect().map(_(0)).toArray
       }
 
-      val (readPartitions, readBatches) = df.queryExecution.sparkPlan.collect {
+      val (readPartitions, readBatches) = df.queryExecution.executedPlan.collect {
         case in: InMemoryTableScanExec => (in.readPartitions.value, in.readBatches.value)
       }.head