There have been allegations of attempted entrapment, obsessive secrecy, over-zealousness, betrayal and cover-up, of rivalries between individuals in the force and between the watchdog institutions overseeing them.

All have been aired in excruciating detail, even as events beyond the hearing room were demonstrating why the full and undivided attention of senior officers was needed elsewhere.

In western Sydney, a disturbed young woman wielding a knife was shot dead by police.

Mid-week Kaldas' fellow deputy commissioner, Catherine Burn, the target of much of his anger, fronted a press conference to reveal two more alleged lone-wolf Islamic extremists preparing to commit acts of butchery. This was enough serious business for any senior police officer to be getting on with.

Yet 24 hours earlier, Burn was having to defend her integrity before the state upper house inquiry , declaring she'd never pursued a vendetta against Kaldas despite being part of a team secretly targeting him for a corruption investigation many years before.

When Burn fronted the terrorism press conference on Wednesday, it was with a "j'accuse" from Kaldas still ringing in her ears.

In a dramatic moment during the hearings on Tuesday, he'd told the committee it was Burn who first raised his name during secret interviews more than a decade ago with a corrupt police officer turned informant, a man variously referred to as "Sea" or "M5".

The informant had proffered a list of supposedly suspect officers to internal affairs investigators but "I was the only one – the single one – who M5 did not actually volunteer or mention", Kaldas said.

"Despite that, I was singled out and specifically asked about by the interviewing team of Ms Burn and another officer."

M5's allegations resulted in a dragnet of surveillance – operation Mascot – being cast over Kaldas and more than 100 others. Kaldas later discovered he was named in no less than 80 secret bugging warrants, which included surveillance of members of his family.

He has accused the former police internal affairs unit, of which Burn was a part, of engaging in "massive wrongdoing and habitual illegal acts".

"For over a decade... our elected politicians, our police ministers, were briefed that I had a cloud over my head and that there was a reasonable suspicion about my integrity," an outraged Kaldas told the committee this week. "[Yet] I held the highest level of clearance from our federal government and was entrusted by our national government and many other nations, our allies, with top-secret information."

Burn defended the use of M5 this week, saying despite the fact that he was a confessed perjurer and criminal, he had helped send several corrupt cops to jail.

She also defended her belief at the time that there was reasonable grounds for Kaldas to be targeted, though she now accepted he had been cleared in subsequent investigations.

But what has stoked the long-simmering anger of Kaldas and many other serving and former officers is the cover-up which they say dogged efforts to get to the bottom of the affair. One such attempt, Task Force Emblems , was stymied by being denied access to key documents.

A fresh inquiry began in 2012 under state Ombudsman Bruce Barbour, but that has been accused by Kaldas of targeting whistleblowers rather than getting to the bottom of the legality or propriety of the original actions of investigators (a charge Barbour has strongly rejected).

The Police Integrity Commission and the NSW Crime Commission – both with enormous powers of their own – are also entangled in the affair, through their involvement with the original surveillance operations.

Professor Mick Kennedy, a former NSW detective and former officer at the Crime Commission, told Fairfax: "What I see in all of this is a total and utter failure of an oversight mechanism to deal with it. It could have been stopped 15 years ago, they could have called people into a room and said, enough is enough, this stops right here... but [agencies] were more concerned about protecting their own brand than anything else... they hid behind immunity and secrecy."

Lawyer David Porter said in a submission to the inquiry that "because of the involvement of the NSW Police Force, the NSW Crime Commission and the PIC in the initial investigations, all of the entities with the resources to conduct active investigations ... had an apprehended conflict of interest".

In what is a second major underlying issue for the inquiry, a former solicitor for the Crime Commission, John Giorgiutti, has also sounded the alarm about the sheer volume of secret warrants being issued to the powerful state agencies for surveillance operations, querying whether the courts are subjecting them to sufficient scrutiny.

Greens upper house MP and former barrister David Shoebridge, one of the most active members of the inquiry, says: "There is this largely pretend oversight by the Supreme Court of applications for warrants and covert surveillance... our court system cannot handle inundating waves of ex parte applications by crime agencies other than by simply rubber-stamping them."

The upper house inquiry will report later this month. Barbour's inquiry, dubbed "Operation Prospect", is continuing to trawl through more than a million pages of documents and won't report until the middle of the year.

In the meantime, the NSW government is desperately hoping that the issue does not insert itself into the state election campaign.

Burn, Kaldas, and their boss, police chief Andrew Scipione, have told the committee that despite the froideur at the senior levels of the force, all are continuing to serve the public to the very best of their ability.

But both Kaldas and Burn have also spoken about the hurt they and their families have suffered. And the issue has deep implications for the succession. Both Burn and Kaldas had been seen as the most likely contenders to replace Scipione when he retires in the near future. Now, no-one can say who will be left standing when the smoke clears.

One source says the best outcome would be a negotiated settlement whereby, if both inquiries vindicate Kaldas' quest for a full accounting of the affair while showing no malice or wrongdoing by Burn, he takes the job for a reduced term, trains her up, and eventually hands over to her.

But that might be asking too much of both deputy commissioners. Kaldas said this week he had forgiven Burn but "I would have preferred [her] to express some regret for what appears to have been poor decision-making early on in her career".

One source who knows the parties well says "it's a like a marriage, if the magic is gone its pretty hard to get that back".

The other underlying issue exposed by the saga has been the dysfunction of police oversight mechanisms, especially the overlapping roles of competing agencies.

Shoebridge says the complaints mechanism is "fundamentally broken", and takes issue with the concept of police investigating police.

He has been impressed with the British  model of a single independent agency handling police corruption and complaints, with its own, independent investigators.

Scipione told the upper house inquiry last week, "My view is this should have been a single agency that had carriage of this investigation ... It is very difficult when you have got three agencies, with all the goodwill in the world, with one starting the bus, one using the brake and one using the accelerator. That does not work."

Shoebridge says "nobody – no government, no minister and no commissioner – has grasped the nettle; that's why we have this sorry mess now".