Cookson hopes to soon announce an agreement with the World Anti-Doping Agency on the framework and delivery of the investigation he promised after deposing Pat McQuaid as head of cycling's world governing body.
A top priority is discovering whether McQuaid, UCI president from 2005 to 2013, and the Irishman's predecessor, Hein Verbruggen, were complicit in doping practices which have blighted the sport. Both men have repeatedly and vigorously denied wrongdoing.
Travis Tygart, the chief executive of the United States Anti-Doping Agency whose investigation into the United States Postal Service team resulted in the downfall of Lance Armstrong, stated earlier this year that he believes the Texan has proof that the UCI was complicit in his drug use.
Cookson hopes once the independent inquiry is under way, it can work quickly to uncover the truth.
"We know a lot of what went on," Cookson told Press Association Sport.
"What I'm really most concerned about is the allegations of the UCI's collusion and cover ups. That's something that we've got to establish fairly quickly.
"It'll take a couple of months to set up (the independent commission).
"(And) it's not going to be over in two or three months; it'll take longer than that. I'm hoping it can be concluded with 12 months."
So determined was Cookson that evidence be preserved that in the minutes after his election in Florence on September 27, he instructed IT equipment and documents from the UCI headquarters in Aigle, Switzerland be seized and securely stored.
"What we wanted to do was make sure nothing was hidden or destroyed that shouldn't have been," Cookson said.
"All the information is there, back-up tapes and copies of back-up tapes from the UCI's computers as far back as we can go, some old laptops, hard drives and so on.
"It is securely and independently stored. The only persons that I will give permission to look at that information will be the people who will be conducting the independent inquiry."
Cookson wants the work of the commission to allow cycling to be able to draw a line in the sand and move on from the past.
"We just need to have as much out on the table as we can," Cookson added.
"And let's put in place structures that will prevent us from repeating those mistakes of the past."
The spectre of the EPO era, when use of the blood-boosting agent was commonplace, resurfaced last week when Canadian Ryder Hesjedal admitted to doping early in his career.
Hesjedal in 2012 won the Giro d'Italia and was widely hailed as a 'clean' winner, which he may well have been, but his confession raised numerous concerns.
The fact his admission comes outside the statute of limitations again raised the prospect of how to punish historical indiscretions. It is one of the many issues the independent inquiry will assess.
Three of Hesjedal's Garmin-Sharp team-mates missed the start of the 2013 season after negotiating six-month suspensions after providing evidence to USADA.
Cookson would speak only generally and not discuss individual cases, but is well aware of the nuances of a system which will not appease everyone.
"The concern is that we find a mechanism that is acceptable to all the bodies," Cookson said.
"(But) not everybody is going to be happy with everything that comes out of this."
Another hope for Cookson is that the inquiry can determine, through "a logical and equitable process of assessment" who is a fit and proper person still to be involved in the sport and "what shall, or shall not, happen to those people who do confess and are genuinely contrite".
Hesjedal was once a team-mate of Armstrong at US Postal.
Armstrong - told by McQuaid he had "no place in cycling" last year - will be offered the opportunity to take part in the inquiry.
However, the 42-year-old may have more immediate concerns, as he fights numerous court cases.
"We are going to offer the same opportunity to everybody and Lance Armstrong will be welcome to give his contribution," added Cookson, who has not spoken to the American.
Cookson believes he is making swift progress five weeks into the job.
The 62-year-old described the election battle with McQuaid as "unnecessarily bitter" and believes those within cycling and the wider sporting world - including the International Olympic Committee - welcomed a change in UCI leadership.
"A lot of people, a lot of organisations have already expressed their support and so my job will be that much easier because we're working with those people, not against them, as the UCI often seemed to be doing in the past," Cookson added.