After losing the case before the High Court, the AG and KCAA moved to the Court of Appeal.
They raised 56 grounds, challenging Justice Roselyn Nambuye's verdict. In their appeal, they claimed, among other things, that she failed to find that African Commuter Services was required to confirm the condition of Busia Airstrip before its pilots flew the ill-fated airplane.
After hearing rival arguments, Justices Wanjiru Karanja, Daniel Musinga and Kathurima M'inoti added Sh362 million on top of the Sh900 million that had been awarded by the High Court. The bill now rose to Sh1.4 billion.
In their verdict, they awarded the airline 50 per cent of the cost of the case in the High Court and Court of appeal. This was on February 7, 2014.
The appellate judges said that after considering other airplane crashes, it was clear that KCAA discriminated African Commuter.
"We agree with this witness and the finding of the learned Judge that the respondent was not accorded equal treatment with other operators who had been faced with similar circumstances," the judges ruled.
"He was clearly discriminated against, purely in our view, because of the status of the passengers involved. There is no doubt that the "permanent" suspension of the respondent's Air Operator Certificate was capricious, punitive and retributive."
Ismael Mohamed Jibril, the owner of African Commuter Service, stated that 5Y-EMJ crashed in Busia while the second one, 5Y-EMK which was also on lease agreement was repossessed and taken back to South Africa.
Africa Commuter Service then sold pane 9L-LCP (9XR-AL) by the end of 2003 and the fourth plane was also repossessed.
The sixth one was sold off to Bukavu the same year, while the seventh one was parked somewhere in Congo for two years.
The remaining one, a 9XR-AB was sold in 2004 as KCAA stuck to its gun that it would not reinstate the license.
Besides Jibril, African Commuter Services called Captain Joe Mutungi as its other witness. Mutungi is one of the pioneer African pilots.
When asked about the suspension of the firm's license following the accident, Mutungi stated that for the 30 years he had been in the aviation industry, he had never come across a situation where an airline's certification was cancelled because of an air accident.
He gave an example of the Kenya Airways accident in Cameroon, the Bluebird jet accident in Kitui in 2004, and the 2000 Kenya Airways accident in Ivory coast.
Despite the accidents, he said, the licenses of the pilots and the airlines were never suspended nor cancelled.
The firm also called an accountant as its third witness. The accountant narrated that his employer ran into losses after the license was cancelled.
To demonstrate this, he explained that between 2002 and 2003 before the license was cancelled the company was making profit.
On the other hand, KCAA called its Director General Chris Kuto and its then manager air traffic services Samwel Henry Odoyo Nyikuli.
Nyikuli admitted that he authored the note to suspend African Commuter's license.
He told the court that the director called him at around 11pm, the day the accident happened, and instructed him to suspend it.
KCAA also called Benjamin Enyenze, its deputy director in charge of air transport department.
However, judges found that his evidence had no value and was not relevant to the dispute.
Justices Wanjiru, Musinga and M'inoti put to task Nyikuli for addressing the wrong company. He was also on the spot why his boss (Kuto) did not sign the latter.
"As stated earlier, it is addressed to the wrong person so the respondent could easily have disowned it; not that it would have changed anything given the minister's directive.
"Secondly, it is not signed by the Director General himself but by one S. H. Nyikuli. Is this countenanced by the Civil Aviation Act," judges observed.
KCAA also claimed that it acted on public interest. Judges were of the view that there was no evidence by KCAA that the Director General delegated his powers to Nyikuli.
They said: "This was a very delicate situation whereby by a stroke of the pen the respondent's entire aviation business was to be grounded to an abrupt halt. It called for more serious consideration and strict compliance with the relevant laws and regulations.
"It definitely needed much more than an improperly addressed, handwritten missive dispatched by way of fax in the middle of the night, and signed by a person who had clearly no authority to do so for lack of proper delegation."
The appellate court was of the view that there was no reason to act in haste as the accident had already happened.
The judges stated that it was prudent to wait the following day, visit the accident scene with experts, collect basic facts on what happened and if need be; suspend the license.
"That way, the blunders of having an unauthorised person purport to suspend the license could have been avoided. The long and short of this is that the Director General did not exercise his discretion prudently as he is enjoined by law to do," the court stated.
The three judges sealed KCAA's fate on February 7, 2014.
Their judgment then stoked up another application before another Bench of the same court.
This time, KCAA asked Justices GBM Kariuki (now retired), Festus Azangalala and Jamila Mohammed to certify their application as that of public importance.
This was a ticket to the Supreme Court. However, the three judges on May 29, 2015 dismissed the application.
Aggrieved, the authority moved to the Supreme Court. Among its arguments was whether it was fair for the public to pay Sh1.4 billion to African Commuter Services following KCAA Director General's delegation of his work to his juniors.
In total, the authority raised 14 grounds that it felt were crucial to the case.
However, the Bench led by Chief Justice David Maraga (now retired), and Justices Jackton Ojwang (retired), Smokin Wanjala, Njoki Ndung'u and Isaac Lenaola unanimously dismissed the application on December 7, 2018.
They found that the law was clear on what is the effect of officers failing to comply with the law while delegating their powers.
"We agree with the Court of Appeal's observation that the intended appeal does not raise an issue where the law requires clarification. The applicant has indeed not demonstrated the uncertainty that this court will need to clear and clarify," the Supreme Court ruled.
But the dispute between KCAA and African Commuter Services did not end at the Supreme Court. The battle now attracted National Bank of Kenya and CFC Stanbic.
The firm asked the High Court to attach KCAA's accounts in the two banks after failing to pay the money.
On the other hand, KCAA sought to have the court to review the Sh1.4 billion decree. It wanted the court to compute the amount.
KCAA claimed that it owed African Commuter Services around Sh601 million.
African Commuter Services in its response told Justice Afred Mabeya that KCAA was abusing the court process. The judge dismissed the application.
There was also a separate application before Justice Joseph Sergon over payment.
In the application, African Commuter Services was philanthropic enough to waive its right to demand costs of the case, both in the High Court and Court of Appeal.
While asking the judge not to attach its accounts in the NBK and CFC, KCAA claimed that its money in the two banks was its operating capital. Justice Sergon found the government agency was lying.
He noted that African Commuter Services had waited for 11 years to be paid, adding that even when the Court of Appeal ordered it to pay, it had not paid a dime.
"In any event, the respondent was not candid with the court. It only alleged that the monies in the subject bank accounts are operating capital.
"To my mind, if the respondent was candid enough, it should have disclosed all the bank accounts that it operates apart from the two garnished and the respective balances thereon or if not, state to the court whether the two accounts are the only accounts it holds," argued Justice Sergon.