In the two years since the Jan. 6, 2021, attack on the Capitol, the Justice Department has undertaken the largest criminal inquiry in its history.Credit…Shuran Huang for The New York Times

WASHINGTON — The investigation into the storming of the Capitol is, by any measure, the biggest criminal inquiry in the Justice Department’s 153-year history.

And even two years after Jan. 6, 2021, it is only getting bigger.

In chasing leads and making arrests, federal agents have already seized hundreds of cellphones, questioned thousands of witnesses and followed up on tens of thousands of tips in an exhaustive process that has resulted so far in more than 900 arrests from Maine to California.

But the inquiry, as vast as it has been, is still far from complete: Scores, if not hundreds, more people could face charges in the year — or years — to come, spread out over the course of many months so as not to flood the courts.

The Capitol siege investigation, as the government likes to call it, has been, among other things, a highly publicized and sophisticated effort to bring to justice extremist groups like the Proud Boys and the Oath Keepers militia. Both played central roles in attacking the Capitol and disrupting a pillar of American democracy on Jan. 6: the lawful transfer of presidential power.

But it has also lumbered on at a quieter level, with a series of less prominent trials and arrests that have touched the lives of more ordinary people: the members of the mob who may not have planned for violence but nonetheless broke into the Capitol that day — many after falling victim to the lies about election fraud spread by President Donald J. Trump.

At the same time, the inquiry into what happened at the Capitol has served as the backdrop to the special counsel investigation that is examining the roles that Mr. Trump and several of his aides and lawyers played in a broader attempt to overturn the results of the election. That investigation, which has so far rested largely on cellphone seizures and grand jury subpoenas, will ultimately have to determine whether Mr. Trump’s norm-shattering efforts to remain in power actually violated any federal laws.

No matter where these inquiries end up, the attempts to fully understand the events leading up to Jan. 6 and to hold accountable those who inspired or took part in them has already tested the Justice Department, straining its resources, pushing it into novel legal territory and exposing it to vehement political attacks.

But over and over, the judges who have overseen criminal cases in Federal District Court in Washington have asserted that the exertions have been worth it.

“People need to ask themselves what conditions could have created that to happen and be honest with yourself when you’re asking the question,” Judge Amit P. Mehta said of Jan. 6 at a hearing in September.

“We cannot function as a country,” he went on, “if people think they can behave violently when they lose an election.”

As of Wednesday, about 950 people had been charged in connection with the storming of the Capitol.

Most of the charges brought so far have been for relatively minor misdemeanors like trespassing or illegally parading in the Capitol, reflecting the fact that hundreds of rioters who went into the building did no damage to property or people. The maximum sentence for these petty offenses is six months in prison, and many defendants charged with them have been given only a few weeks in jail or have faced no time at all.

About 280 people have been charged with the more serious crime of assaulting or resisting the police, including about 100 who are facing additional charges of using a dangerous or deadly weapon. While prosecutors say only a handful of rioters were carrying — or talked about carrying — firearms on Jan. 6, an impressive list of makeshift weapons was used in the attack: flagpoles, bear spray, two-by-fours, metal poles, collapsible batons, stun guns, a hockey stick, even a skateboard.

The assault cases have yielded the stiffest penalties so far. In September, Thomas Webster, a former New York City police officer convicted of attacking an officer at the Capitol with a flagpole, was sentenced to 10 years in prison, the most severe sentence yet in a Capitol riot case.

One month later, Albuquerque Cosper Head, a Tennessee resident, was sentenced to seven and a half years in prison after pleading guilty to dragging Michael Fanone, a police officer, into an angry pro-Trump crowd that brutally assaulted him and attacked him with a stun gun.

Nearly 300 people have faced an unusual charge: obstruction of an official proceeding in front of Congress. Prosecutors have used this count — originally intended to prohibit things like shredding documents or tampering with witnesses in congressional inquiries — to describe how the mob chased lawmakers out of the Capitol on Jan. 6, disrupting the final certification of the election.

Last month, a federal appeals court was asked to toss the charge in all of the Jan. 6 cases by defense lawyers who say it was improperly used. The lawyers argued that the law was misapplied to the Capitol riot cases and used to criminalize behavior that too closely resembled protest protected by the First Amendment.

The government has racked up an impressive record in its Jan. 6-related trials, all of which have taken place in the federal courthouse in Washington despite repeated efforts by defense lawyers to have them moved to jurisdictions thought to be friendlier. Of the 45 defendants who have gone to trial so far, all but one — a former government contractor from New Mexico — have been convicted of most of the charges they were facing.

All trials are, in a sense, performances, and prosecutors in the Capitol riot trials have often used the proceedings to make larger points about Jan. 6 or to expose some vivid aspect of that day.

In the most prominent trial to date, Stewart Rhodes, the founder and leader of the Oath Keepers, was convicted along with a lieutenant of seditious conspiracy but was acquitted of other conspiracy charges. The mixed verdict suggested something crucial about Jan. 6: that even though the jury seemed to believe the attack on the Capitol unfolded more or less spontaneously, it also believed that Mr. Rhodes had a broader plan in place to use physical force to keep Mr. Trump in power.

While the Oath Keepers trial often delved into Mr. Rhodes’s conspiratorial mind-set, the police assault trials have arguably been the most dramatic, featuring gripping testimony about the hand-to-hand combat that raged for hours between rioters and officers. Much of that testimony has come from officers themselves during evocative and emotional turns on the witness stand.

In September, former Sgt. Aquilino Gonell of the Capitol Police testified that the shoulder injury he suffered that day changed his life forever, robbing him of his job, his facility at basketball and his ability to coach his son in sports. At a different trial in August, former Officer Daniel Hodges described the terror of being crushed by the mob in a door at the lower west terrace of the Capitol.

“From my experience, it looked like something out of medieval times, where you have one huge force clashing with another opposing force,” a third officer, Eugene Goodman, said at yet another trial. “I’ve never seen something like that ever.”

Almost every day, prosecutors bring a few more Capitol riot cases, some of which have been under investigation for nearly two years. Given the time lag and the steady trickle of new filings, many defense lawyers have said that their clients who were at — or especially those who were inside — the Capitol on Jan. 6 are still looking over their shoulders, waiting to be charged.

It is impossible to know for sure how many new cases could be filed in the weeks and months to come, but prosecutors have long said that as many as 2,000 people broke the law on Jan. 6 by entering the Capitol or by committing other crimes like assaulting officers on the Capitol grounds. Whatever the number ends up being, it is significant enough that the federal bench in Washington has been told to expect a surge of cases, according to several people familiar with the matter.

“Our work is far from over,” Attorney General Merrick B. Garland said in a statement issued on Wednesday.

Jacquelyn Starer, a Massachusetts doctor, was charged last month, and her case is instructive.

The F.B.I. first received a tip about Dr. Starer, 68, five days after the Capitol was stormed, but did not arrest her until Dec. 20, 2022 — some 23 months later. The story of what happened in between, contained in the documents used to bring the charges, suggests both the thoroughness and the methodical pace of the bureau’s investigation.

One of the F.B.I.’s earliest steps was tracking down Dr. Starer’s photo from the Massachusetts Registry of Motor Vehicles. Agents also got the records from her stay at a Washington hotel and obtained the subscriber information for her cellphone, using it to determine that the phone had connected with a cell site near the Capitol on Jan. 6.

The F.B.I. had another pool of evidence in the thousands of hours of video footage it collected from the Capitol attack.

Surveillance cameras at the building showed that Dr. Starer went inside through the east Rotunda doors at 2:51 p.m. that day, court papers say. Body camera footage from the police, the papers say, showed her balling up a fist and punching an officer just eight minutes later.

Investigators ultimately interviewed the officer, known in the papers only as M.B. The officer recalled that a blonde woman, fitting Dr. Starer’s description, struck her on the left side of her head.

Robert Sheketoff, Ms. Starer’s lawyer, said that waiting a long time for charges to be filed is a mixed blessing that gives defendants the opportunity to keep living a normal life — albeit one cast in shadow.

“It’s both a good thing and bad thing,” Mr. Sheketoff said. “A double-edged sword.”

Despite the F.B.I.’s tenacity in pursuing Capitol riot cases, several aspects of the investigation remain unresolved.

Chief among the mysteries is the identity of the person who left pipe bombs on Jan. 5, 2021, outside the Democratic and Republican Party headquarters, blocks from the Capitol. The bombs, which had crude mechanical timing devices, were discovered on the afternoon of Jan. 6, causing havoc in Washington.

Investigators have periodically released information about the bomber, including videos showing a person dressed in gloves and a hoodie, and a map drawn from surveillance camera footage showing the route the person walked while placing the bombs. Still, the F.B.I. has been unable to identify whomever was responsible.

While much of the bureau’s efforts remain shrouded in secrecy, some unresolved threads of its inquiry have emerged from the shadows.

One of those concerns the ways in which a “Stop the Steal” protest of the 2018 Senate race in Florida may have served as a model for what happened in Washington on Jan. 6. In recent months, prosecutors have been asking questions about key players in the earlier demonstration — among them, the political operative Roger J. Stone Jr. and Jacob Engels, an associate of Mr. Stone connected to the Proud Boys — in an effort to determine whether the tactics used in Florida were also used at the Capitol.

Some people who played central roles in the Capitol attack even remain at large and unidentified in spite of the array of high-tech tools — like cellphone tracing and facial recognition — at the F.B.I.’s disposal. These mysterious figures have been studied closely by an army of online sleuths known as sedition hunters who have tracked their movements during the attack through thousands of hours of video.

At some point, the F.B.I. might track them down and arrest them. But for now, they are largely known by the colorful hashtag names given to them by amateur investigators — monikers like #LemonyKickIt, #NWScaffoldCommander and #SandStoneHoodie.