Hi onlyadrafter,
I give it a try, and after some modifications I got a chart that looks the way that I wanted. This is how the macro works for me:
Option Explicit
Dim LATEST, TOTAL, MOVE_OVER, PULSE, MY_VALUE, ADD_VALUE As Variant
Dim A_VALUES, B_VALUES, C_VALUES As Variant
Dim MY_VALUES(1000) As Variant
Dim ADD_VALUES(1000) As Variant
Sub Macro1()
'
' Macro1 Macro
'
' Keyboard Shortcut: Ctrl+s
'
LATEST = 0
TOTAL = 0
MOVE_OVER = 0
PULSE = 0
Columns("E:G"

.ClearContents
For MY_VALUE = 1 To Range("a65536"

.End(xlUp).Row
'MY_VALUES(MY_VALUE) = MY_VALUES(MY_VALUE) + Range("A" & MY_VALUE).Value
MY_VALUES(MY_VALUE) = Range("A" & MY_VALUE).Value
Range("E65536"

.End(xlUp).Offset(1, 0).Value = MY_VALUES(MY_VALUE)
'Range("E65536"

.End(xlUp).Offset(1, 0).Value = MY_VALUES(MY_VALUE)
If PULSE = 0 Then
PULSE = 1
Else
PULSE = 0
End If
Range("F65536"

.End(xlUp).Offset(1, 0).Value = PULSE
'Range("F65536"

.End(xlUp).Offset(1, 0).Value = PULSE
MOVE_OVER = MOVE_OVER + 2
Next MY_VALUE
MOVE_OVER = 2
Range("G2"

.Value = MY_VALUES(1)
TOTAL = MY_VALUES(1)
For ADD_VALUE = 1 To Range("E65536"

.End(xlUp).Row - 2
TOTAL = TOTAL + Range("e1"

.Offset(MOVE_OVER, 0).Value
Range("G65536"

.End(xlUp).Offset(1, 0).Value = TOTAL
MOVE_OVER = MOVE_OVER + 1
Next ADD_VALUE
A_VALUES = "=Sheet2!R2C7:R313C7"
B_VALUES = "=Sheet2!R2C7:R313C7"
C_VALUES = "=Sheet2!R2C6:R313C6"
Charts.Add
ActiveChart.ChartType = xlXYScatterLines
ActiveChart.SetSourceData Source:=Sheets("Sheet2"

.Range("F2:F313"

, PlotBy:=xlColumns
ActiveChart.SeriesCollection(1).Values = A_VALUES
ActiveChart.SeriesCollection(1).XValues = B_VALUES
ActiveChart.SeriesCollection(1).Values = C_VALUES
ActiveChart.Location Where:=xlLocationAsObject, Name:="Sheet1"
ActiveChart.HasLegend = False
End Sub
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The lines that I commented out, why did you repeat them?