You can use the OnFilter event. This code removes every event that doesn't come from the users chosen department or the sites main calendar.

<EPiServer:Calendar ID="CalendarList" PageTypeID="28" runat="server" NumberOfDaysToRender="360" ExpandAllDays="false" OnFilter="FilerEvents">

 Code behind:

protected void FilerEvents(object sender, EPiServer.Filters.FilterEventArgs e)
{
 PageDataCollection Pages = e.Pages;
 PageData MainCalender= GetPage((PageReference)StartPage["ShowCalendarFrom"]);

 for (int i = 0; i < Pages.Count; i++)
 {
  PageData iPage = Pages[i];
  if (iPage.ParentLink != MyDepartment.PageLink&&iPage.ParentLink!=MainCalender.PageLink)
  { 
   Pages.RemoveAt(i);
   i--;
  }
 }
}

Thanks very much.

I would like to know what is "MyDepartment" in the above code?

 

MyDepartment is a PageData object that I set to the calendarpage that my users have chosen.
In my site there is a lot of different calendapages. That's why I'm comparing the parent link in the events.
You could also choose to use a property on every event instead. And then you could compare to that.
if(iPage["OfficeName"]!="Huvudkontoret")
Pages.remove.....