Any Unknown or Unlisted Aircraft Manufacturer
Flight Crew Air Transport Pilot (ATP); Flight Crew Instrument; Flight Crew Multiengine
Flight Crew Last 90 Days 30; Flight Crew Total 8700; Flight Crew Type 800
Situational Awareness
Deviation - Track / Heading All Types; Deviation / Discrepancy - Procedural Clearance; Deviation / Discrepancy - Procedural Published Material / Policy
Air Traffic Control Issued New Clearance; Flight Crew Returned To Clearance
Procedure; Environment - Non Weather Related; Human Factors
The mission on this day was a little unusual and because of the recent COVID pandemic our flying has diminished substantially. We had to fly from ZZZ to ZZZ1 then fly and empty leg to ZZZ2. We picked up passenger in ZZZ2 and went back to ZZZ1 to pick up additional passenger before returning to base in ZZZ. We had about a 1.5-2 hour break while in ZZZ2 for lunch.To simplify operation we decided that I would be Pilot Monitoring for the first two legs; ZZZ to ZZZ1 and ZZZ1 to ZZZ2. I would be Pilot Flying for the last two legs. To help expedite our ground time I opted to load up our upcoming flight plans in the secondary flight plan so after we landed and received our clearance all we had to do was activate it and verify it.I think this is where something went wrong. I loaded up the flight plan for ZZZ2 to ZZZ1 while we were flying to ZZZ2. I opened our flight plan and loaded it up the way we filed it; route. When we got to ZZZ2 attempting to land on Runway XX we experienced wind shear causing us to go-around. After a successful recovery we were able to come back and land without further incident. The reason I mention the wind shear event is because it changed our planning on departure runways.After lunch we loaded up our passenger and called ZZZ2 clearance to change our runway from XYL to XX because we experienced wind shear on the way out. We thought it would be prudent to depart with more of a headwind component than a crosswind component. This caused a significant change in our flight plan. We would now depart Runway XX via the ZZZZZ to ZZZ3 [Jet route] thence ZZZZZ1 for the arrival. I believe this is where the error happened. I am not sure if it was a human factor error or a computer error. We both looked at the FMS and noticed a few discontinuities. After discussing them together we cleared up the issues and launched. While in cruise the aircraft flew from ZZZZZ1 to ZZZZZ2 and somehow [6 additional intersections] were missed. A few miles abeam ZZZZZ3 Center requested a 20 degree turn to the right and asked us if we were on an arrival. We responded affirmative. ATC then told us that we should have been flying over ZZZZZ3 at the time and said that it was ok; we would fly back into their airspace and then be cleared directly to ZZZZZ2. After that everything was normal all the way to our destination and to our home base.We discussed this in detail and determined that we should have looked at each fix to verify instead of just looking at the flight plan page. Normally this is something we do but because of recent events we chocked it up to complacency due to lack of routine. Obviously this is no excuses for pilot error but I thought it important to share my experience because it is something that can easily happen with the way our flight plan is displayed in the FMS. You can verify your route easily a few different ways in a few different formats. I am thinking; hypothesizing; guessing what happened was in the secondary flight plan the routing was [route] ZZZZZ1.ZZZZZ2 but when we got our route change due to the runway we missed an important part. I think with the change the FMS read ZZZZZ. [route] ZZZZZ1 ZZZZZ2 (note the lack of the period; I think the route in the FMS was [route] ZZZZZ1 direct to ZZZZZ2). This cause the airplane to go from ZZZZZ1 direct to ZZZZZ2 and not actually on the arrival. In the future it is important for any routing but especially complex departures and arrivals to verify each fix. Not just verify they are in the flight plan page.
The other pilot (PF) programmed the FMS from an earlier flight and stored it.  The actual clearance we received was different then what was filed; SOP changes had to be made.  It was done rapidly by him and I failed to check the change against the chart.  For some reason when the change was made; it didn't load the entire arrival but just the initial fix was flown to (ZZZZZ1) then it went direct to ZZZZZ2 instead of flying the fixes in between.  ATC called to query us (as we were off route).  We immediately requested a heading; corrected and reloaded the approach and got back on course.  We briefed after the flight and adopted a full review procedure when storing routes (especially when unfamiliar).
Pilots reported entering the incorrect routing in the FMS resulting in a track heading deviation.