diff --git a/src/atcore.cpp b/src/atcore.cpp
--- a/src/atcore.cpp
+++ b/src/atcore.cpp
@@ -562,7 +562,6 @@
     } else {
         pushCommand(GCode::toCommand(GCode::M104, QString::number(extruder), QString::number(temp)));
     }
-    temperature().setExtruderTargetTemperature(temp);
 }
 
 void AtCore::setBedTemp(uint temp, bool andWait)
@@ -572,7 +571,6 @@
     } else {
         pushCommand(GCode::toCommand(GCode::M140, QString::number(temp)));
     }
-    temperature().setBedTargetTemperature(temp);
 }
 
 void AtCore::setFanSpeed(uint speed, uint fanNumber)
diff --git a/src/printthread.h b/src/printthread.h
--- a/src/printthread.h
+++ b/src/printthread.h
@@ -101,5 +101,53 @@
      * @brief end the print
      */
     void endPrint();
+
+    /**
+     * @brief injectCommand Attempt to inject a Command from the currently printing file.
+     *
+     * One of the following on a line that starts with ';-' \n
+     * example line ;-Message: Hello \n
+     *
+     * - Pause: ppc\n
+     *   Pause the print job and then run the comma seperated commands after pausing the job.\n
+     *     + ppc: A comma seperated list of Commands to send after pause. ex(G91, G0 Z1, G90, G1 X0 Y195)\n
+     *\n
+     * - Extruder %Temperature:newTemp,extnum,wait \n
+     *   Set extruder temperature. \n
+     *     + newTemp: new target temperature. \n
+     *     + extnum: Extruder number you want to Heat. Starting at 0. \n
+     *     + wait: ignore commands until the target is reached. [true | false] \n
+     *\n
+     * - Bed %Temperature: newTemp,wait \n
+     *   Set the bed temperature. \n
+     *      + newTemp: new target temperature \n
+     *      + wait: ignore commands until the target is reached. [true | false] \n
+     *\n
+     * - Fan Speed:newSpeed, fanNum \n
+     *   Set the Fan speed. \n
+     *     + newSpeed: new fan speed. \n
+     *     + fanNum: Fan number. Starting at 0.\n
+     *\n
+     * - Print Speed:newSpeed \n
+     *   Set the printer speed. \n
+     *    + newSpeed: the print speed. 100= movement speed defined in file. \n
+     *\n
+     * - Flow Rate:newRate \n
+     *   Set the flow rate \n
+     *    + newRate: the flow rate. 100 = flow rate defined in file. \n
+     *\n
+     * - Message:message \n
+     *   Show a message the printer's LCD \n
+     *    + message: the message to print. \n
+     *\n
+     * - Command:command \n
+     *   Inject your own command. Command are sent as is. Be sure your line is correct. \n
+     *    + command: Commands to inject \n
+     */
+    void injectCommand(QString command);
+
+    /**
+     * @brief d: Private storage for the thread
+     */
     PrintThreadPrivate *d;
 };
diff --git a/src/printthread.cpp b/src/printthread.cpp
--- a/src/printthread.cpp
+++ b/src/printthread.cpp
@@ -22,6 +22,8 @@
 */
 #include <QTime>
 #include <QLoggingCategory>
+#include <QCommandLineOption>
+#include <QCommandLineParser>
 
 #include "printthread.h"
 
@@ -40,6 +42,16 @@
     QString cline;                      //!<@param cline: current line
     AtCore::STATES state = AtCore::IDLE;//!<@param state: printer state
     QFile *file = nullptr;              //!<@param file: gcode File to stream from
+    QList<QCommandLineOption> options = {
+        {QCommandLineOption(QStringLiteral("pause"))},
+        {QCommandLineOption(QStringLiteral("extruder temperature"))},
+        {QCommandLineOption(QStringLiteral("bed temperature"))},
+        {QCommandLineOption(QStringLiteral("print speed"))},
+        {QCommandLineOption(QStringLiteral("fan speed"))},
+        {QCommandLineOption(QStringLiteral("flow rate"))},
+        {QCommandLineOption(QStringLiteral("message"))},
+        {QCommandLineOption(QStringLiteral("command"))}
+    };  //!<@param options: injectable commands.
 };
 
 PrintThread::PrintThread(AtCore *parent, QString fileName) : d(new PrintThreadPrivate)
@@ -80,7 +92,7 @@
         while (d->cline.isEmpty() && !d->gcodestream->atEnd()) {
             nextLine();
         }
-        if (!d->cline.isEmpty()) {
+        if (!d->cline.isEmpty() && d->core->state() != AtCore::PAUSE) {
             qCDebug(PRINT_THREAD) << "cline:" << d->cline;
             emit nextCommand(d->cline);
         }
@@ -96,6 +108,9 @@
     }
 
     case AtCore::PAUSE:
+        if (d->cline.startsWith(QStringLiteral(";-"))) {
+            nextLine();
+        }
         break;
 
     default:
@@ -126,6 +141,9 @@
     qCDebug(PRINT_THREAD) << "progress:" << QString::number(d->printProgress);
     emit(printProgressChanged(d->printProgress));
     if (d->cline.contains(QChar::fromLatin1(';'))) {
+        if (d->cline.startsWith(QStringLiteral(";-"))) {
+            injectCommand(d->cline);
+        }
         d->cline.resize(d->cline.indexOf(QChar::fromLatin1(';')));
     }
     d->cline = d->cline.simplified();
@@ -150,3 +168,44 @@
         connect(d->core, &AtCore::stateChanged, this, &PrintThread::setState, Qt::QueuedConnection);
     }
 }
+
+void PrintThread::injectCommand(QString command)
+{
+    //remove the ;
+    command.remove(0, 1);
+    command.prepend(QStringLiteral("0:"));
+    QStringList cmd = command.split(QLatin1Char(':'));
+    cmd.replace(1, cmd.at(1).simplified().toLower());
+    cmd.replace(2, cmd.at(2).simplified());
+
+    QCommandLineParser parser;
+    parser.setSingleDashWordOptionMode(QCommandLineParser::ParseAsLongOptions);
+    parser.addOptions(d->options);
+
+    qCDebug(PRINT_THREAD) << "attempting to inject " << cmd;
+    parser.process(cmd);
+
+    if (parser.isSet(QStringLiteral("pause"))) {
+        d->core->pause(parser.positionalArguments().at(0));
+    } else if (parser.isSet(QStringLiteral("extruder temperature"))) {
+        QStringList args = parser.positionalArguments().at(0).split(QLatin1Char(','));
+        bool wait = QString::compare(args.at(2).simplified(), QStringLiteral("true"), Qt::CaseInsensitive) == 0;
+        d->core->setExtruderTemp(args.at(0).toInt(), args.at(1).toInt(), wait);
+    } else if (parser.isSet(QStringLiteral("bed temperature"))) {
+        QStringList args = parser.positionalArguments().at(0).split(QLatin1Char(','));
+        bool wait = QString::compare(args.at(1).simplified(), QStringLiteral("true"), Qt::CaseInsensitive) == 0;
+        d->core->setBedTemp(args.at(0).toInt(), wait);
+    } else if (parser.isSet(QStringLiteral("print speed"))) {
+        d->core->setPrinterSpeed(parser.positionalArguments().at(0).toInt());
+    } else if (parser.isSet(QStringLiteral("fan speed"))) {
+        d->core->setFanSpeed(parser.positionalArguments().at(0).toInt(), parser.positionalArguments().at(1).toInt());
+    } else if (parser.isSet(QStringLiteral("flow rate"))) {
+        d->core->setFlowRate(parser.positionalArguments().at(0).toInt());
+    } else if (parser.isSet(QStringLiteral("message"))) {
+        d->core->showMessage(parser.positionalArguments().at(0));
+    } else if (parser.isSet(QStringLiteral("command"))) {
+        d->core->pushCommand(parser.positionalArguments().at(0));
+    } else {
+        qCDebug(PRINT_THREAD) << "Attempted to inject unknown command: " << parser.positionalArguments();
+    }
+}