Date: 201811
Local time of day: 1801-2400
Location: TUS.Airport, AZ
Aircraft: Fighting Falcon F16
Operator: Military
Flight plan: IFR
Flight phase: Takeoff / Launch
Airspace: Class C TUS
ATC / advisory: Tower TUS
Second aircraft: Fighting Falcon F16
Reporter organization: Government
Reporter function: Local; Handoff / Assist; Supervisor / CIC
Reporter qualification: Air Traffic Control Fully Certified
Human factors: Situational Awareness; Workload; Communication Breakdown; Distraction
Anomaly: ATC Issue All Types; Conflict Ground Conflict; Less Severe; Deviation / Discrepancy - Procedural Clearance; Ground Incursion Runway
Detector: Person Flight Crew
When detected: In-flight
Result: Flight Crew Requested ATC Assistance / Clarification
Contributing factors: Aircraft; Human Factors; Staffing
Primary problem: Staffing

Narrative: I was the only CPC in the building; working LC1; LC2; LA; and CIC; with our two lowest time developmentals beside me in GC and FD/CD. A CPC came in early to work credit; and I told him to get plugged in. A call from the supervisors' office requested him downstairs for a briefing; and I told him to call back downstairs and say he was needed for the operation. Downstairs overrode me; and added that a second CPC had also arrived early for credit but was being held downstairs for the briefing as well.Several minutes later; I cleared Aircraft X two-ship for takeoff with Aircraft Z several miles out. I did not see or hear that Aircraft Y [part of Aircraft X's flight] had aborted takeoff partway down the runway; and I was too task-saturated with traffic and phone calls to notice him. There is certainly a chance he was behind the beam that blocks a portion of the runway directly in front of the LC1 position. I was further distracted by the extremely unusual circumstance of Aircraft X coming back to my frequency off the departure end and asking to stay with me to high key. I asked if it was for both aircraft or just a single; and he was fairly nonchalant in responding 'Yeah; I'd just like to check on my wingman'. Again; not something that in anyway don't my attention to the fact that his wingman was still on the runway. While attempting to coordinate Aircraft X's request with Arrivals and Departures; I was able to make out part of Aircraft Z's transmission over the loudspeaker asking if he was cleared to land. Again; not knowing about Aircraft Y; I again cleared Aircraft Z to land. Our newest developmental made a comment as Aircraft Z was rolling out that he was probably asking because of the [aircraft] on the runway. This was the first moment I became aware Aircraft Y had not taken off. Even once I was alerted to it; actually seeing him out the window took a moment because they are almost perfectly runway colored anyway.Well; clearly all these positions combined during the middle of the day with the Air National Guard out and still departing is not a safe situation. But that isn't a procedure change. We already know that; it's been talked about many times. I really don't like the feeling of throwing anyone under the bus; but the fact is I was the lone CPC/CIC in the building with three FLM's downstairs; and when additional CPC's came in early to help they were kept out of the operation despite my protest. I had multiple frequencies; a mix of arrivals and departures; as well as at least one phone call about another aircraft. We spend too much time operating this way; and it is just too many tasks to balance when something goes awry.




Synopsis: TUS Tower controller reported not noticing a rejected takeoff; due to heavy workload from combined sectors and lack of staffing; and landing traffic causing runway conflict with the RTO aircraft.