Cycling: Sport's Eliot Ness trains his sights on Armstrong

If you're a famous American athlete suspected of doping, then the hound from hell must seem like a benign poodle compared to Jeff Novitzky.

Just ask Barry Bonds, baseball's home run king, whose perjury trial begins in two months' time. Or Marion Jones, the disgraced superstar of the 2000 Olympics who spent six months behind bars. Or Lance Armstrong, perhaps the most famous American athlete of them all.

The notion that the seven-time winner of the Tour de France might have used performance-enhancing drugs is not exactly new. Rumours about Armstrong have been swirling for years, not least because of the assumption, borne out by scandal after scandal, that no one at the pinnacle of cycling is clean. But a long piece this month in the magazine Sports Illustrated – that appeared at the very moment that Armstrong was wrapping up his professional career in Australia – set out the familiar case against him, and added some new elements of its own.

These latter include allegations that Armstrong maintained ties with the controversial Italian sports physician Michele Ferrari, as well as further claims from former team-mates and colleagues that they saw him with drugs, and tests from the 1990s showing that Armstrong's testosterone-epitestosterone ratios were at levels that suggested doping. There is also the suggestion that the cyclist might have had access to HemAssist, a since-discontinued drug that boosts oxygen levels in human blood, and whose traces quickly disappear from the body.

Armstrong has denied these allegations as he has denied every allegation in the past, claiming that his accusers, not a few of them embroiled in drug scandals, had no credibility, and pointing out that throughout his career he had never failed an official drug test.

The differences today however are two. The first is Armstrong's former team-mate Floyd Landis, stripped of his 2006 Tour de France title after failing a drug test. Landis went as far as writing his own book protesting his innocence, but abruptly changed his story last May, admitting not only that he had doped, but accusing Armstrong of doing so, too.

At which point, enter the second factor that changed everything: Novitzky. Armstrong's problem now is not confined to charges plastered over a French newspaper, or a book detailing his alleged transgressions. It is a full-scale probe by the US government, led by one of its most formidable and implacable investigators.

Today, Novitzky is a special agent for the US Food and Drug Administration, but in his previous career at the Internal Revenue Service he cracked the Balco scandal, exposing how a small San Francisco Bay nutritional supplement company had supplied baseball, football and track and field stars with the most sophisticated drugs.

The Balco case led to the downfall of Jones and the British sprinter Dwain Chambers among other athletes. Bonds was but the most celebrated of the baseball stars implicated in the affair, that laid bare the extent of the cheating at the top levels of America's venerable "national pastime". Novitzky's methods have become legendary – how he would go through rubbish bins at Balco at the dead of night to assemble evidence, how once he has a target in his sights he does not let go. His questioning was "like a Cold War investigation," said a key witness in the case Novitzky has helped build against Roger Clemens, one of baseball's greatest ever pitchers, who last year was charged with perjury, for denying to Congress that he used performance-enhancing drugs.

Novitzky's personal appearance has only added to the legend. He is thin and bean-pole tall, at 6ft 6 ins, with a shaven bald head. Many have likened him, in style if not physique, to Eliot Ness, the relentless and incorruptible pursuer of Al Capone in the 1930s, who finally nailed the gangster for tax evasion. He has been criticised too, for abusing his powers and violating the constitutional rights of suspects. Some simply wonder whether, when the public finances are under pressure as never before, it is justifiable to spend tens of millions of dollars investigating star athletes who may have cheated but broke no laws in doing so.

The Armstrong case raises that quandary in especially painful form. Bonds, whether or not he is ultimately found guilty in the trial which begins on 21 March, has never been a popular figure, while Jones's successes as a sprinter were always coloured by the suspicion they were artificially aided.

This time however Novitzky's target is a national hero, a survivor of testicular cancer who came back to compile an almost unbelievable record in one of the most gruelling sporting events on earth – a man as famous for the yellow plastic "Livestrong" bracelets issued by the cancer-fighting Lance Armstrong Foundation as for the yellow jersey he made his personal property at the Tour de France. And the moment of truth, it would seem, is fast approaching.

Novitzky's investigation took off in earnest after the Landis allegations became public. His inquiries have taken the investigation around the world. Last summer a grand jury was empanelled to hear the case. Grand jury deliberations are completely secret, but a decision on whether to issue indictments may come within a few months, even weeks.

As with other athletes accused of drug cheating and who have been convicted, like Jones, or who face trial like Bonds, the point at issue with Armstrong is not so much whether they cheated; what a Tour de France cyclist ingests or injects into himself is not a matter of overwhelming interest to the US justice system.

These cases turn criminal when the athlete lies about drugs under oath, or when it emerges he (or she) might have distributed them to others (in which case trafficking charges could arise). It is also reported that in Armstrong's case, it is being examined whether he defrauded the government, as a long-time member of the US Postal Service team, sponsored indirectly by the US government, should it be established that, for all his denials, he was a drug cheat.

If Armstrong were to be indicted, the Bonds trial, at which other top baseball players are likely to testify, could be a preview. Much will be made of the admissibility of evidence, and much may hinge on whether Bonds' trainer, Greg Anderson, maintains his refusal to testify (and once again faces jail for contempt of court). And even if he is convicted, Bonds may not face jail. Last October the cyclist Tammy Thomas was spared prison, sentenced to six months of home confinement even though she had been convicted of perjury for lying about steroid use.

But ultimately, it is Armstrong's reputation and legacy that is at stake. Marion Jones, said Lamine Diack, president of the IAAF, would be remembered as "one of the biggest frauds in sporting history". A guilty Armstrong would surely be an even greater one. That perhaps was the point that Bono, the Irish singer, was making in an enigmatic tweet to Armstrong when the Landis accusations broke: "Sometimes my friend, the lie is ugly but the truth is unbearable."