As the New York-bound El Al jet cruised through the darkness last Dec. 20, exhausted U.S. investigators quietly celebrated the successes of their trip: Israeli officials implicated in the Jonathan Jay Pollard spy case finally had been questioned, Israel had returned the classified U.S. documents, and Israeli leaders had pledged full cooperation.

Yet the investigators were still nagged by suspicions that they hadn't been told the full story despite nine days of sleuthing in Israel.

As far as the Israeli government was concerned, the embarrassing affair was drawing to a close. "I believe," Israeli Defense Minister Yitzhak Rabin said, "that the case on our part is closed." The State Department expressed similar sentiments by praising Israel's "full cooperation" and predicting a resumption of the "deep friendship" between the two nations.

In fact, the case was a long way from closed. During the first five months of 1986, federal prosecutors directed FBI agents to fan out across the United States to interview scores of witnesses and undertake "classic, white-collar crime" paper chases, as one official put it. Investigators sifted through reams of classified documents, credit card receipts, telephone bills and bank records.

Months after those nagging doubts on the El Al flight, investigators discovered that their skepticism was well-founded. Pollard agreed to talk, and implicit in his confession was a deeper Israeli role in the case and a more extensive spying operation than had been previously acknowledged.

As those revelations became public when the former civilian Navy counterintelligence analyst pleaded guilty to a federal espionage conspiracy charge, once again the Pollard case threatened to strain U.S.-Israeli relations -- something State Department and Israel officials thought had been averted in December.

And the long-simmering feud between the Justice and State departments over the Pollard case erupted again as State officials moved to minimize the significance of the new information and Justice officials pressed for a fuller accounting from Israel.

Israeli Justice Minister Yitzhak Modai, who met yesterday with Secretary of State George P. Shultz and Attorney General Edwin Meese III, told reporters that his government wants to see the Pollard investigation "accelerated to the maximum." But he called allegations of a wider Israeli involvement in the case "a lie."

Israel Embassy spokesman Yosef Gal yesterday declined to answer specific questions about the case, and referred a reporter to a May 31 statement issued by the embassy that the Pollard incident "was an unauthorized deviation from the clear-cut Israeli policy of not conducting any espionage activities whatsoever in the United States."

Among the questions U.S. officials say remain unanswered:What happened to the internal Israeli inquiry that Prime Minister Shimon Peres promised last December?

"The government of Israel is determined to spare no effort in investigating this case thoroughly and completely and in uncovering all of the facts to the last detail, no matter where the trail may lead," Peres said then. Has anyone implicated in the case been punished, as the Peres government pledged?

"If the allegations are confirmed, those responsible will be brought to account, the unit involved in this activity will be completely and permanently dismantled," Peres said in December.

Israeli officials have said the unit implicated in the Pollard operation has been abolished.

But U.S. officials repeatedly note that Raphael (Rafi) Eitan, the former Israeli intelligence official alleged to have run the operation, was recently appointed chairman of the board of an Israeli government-owned chemical company, and Col. Aviem (Avi) Sella, allegedly Pollard's first contact, was promoted to brigadier general. Two others implicated in the case, a former secretary at the Israeli Embassy here and a former New York-based science consul, reportedly also have been given attractive new jobs in the Foreign Service. Why was the role of Sella not disclosed to U.S. officials during their visit to Israel last December?

His involvement was revealed by Pollard. Similarly, it was Pollard, not the Israeli government, who told investigators of his Israeli handlers' plan to deposit $300,000 for him in a Swiss bank account over 10 years. Pollard also revealed that his contacts had obtained an Israeli passport for him in the name of "Danny Cohen." The passport was to be used by Pollard when the operation ended and he moved to Israel, prosecutors said. Why was Pollard, apparently in response to a request from one of his Israeli handlers, looking into missile systems for possible sale to Iran?

According to a letter found by investigators, which Pollard had written to one of his Israeli handlers, the analyst said he was looking at missile systems designed or manufactured by non-communist foreign countries that "might be available for sale to Iran?"

Israel in the past has sold spare military parts to Iran, which has been at war with Iraq for nearly six years. But Israeli officials have said the sales stopped long ago after the State Department objected. Will Israel identify other Israelis suspected of being involved in the Pollard operation?

On at least two occasions when Pollard met with his handlers, once at the suburban Maryland home of an Israeli diplomat whose identity was withheld by prosecutors and also while Pollard was in Israel, another Israeli known only as "Uzi" was present, according to court documents. U.S. officials said they do not know the identity of Uzi.

Investigators would also like to know who assisted in copying documents Pollard supplied to his handlers.

Prosecutors said Pollard usually delivered the material to Irit Erb, then a secretary at the Israeli Embassy here, twice a month for more than a year at her apartment. Sources said the apartment was in the Van Ness East condominiums at 2939 Van Ness St., NW, close to the Israeli Embassy.

Pollard's handlers also maintained another apartment in Erb's building that housed "sophisticated copying and photographic equipment," prosecutors said, and "unidentified persons in the bedroom of the apartment would . . . copy the documents . . . . "

Last Nov. 20, the day before Pollard was arrested outside the Israeli Embassy, Erb, who sources said did not have diplomatic immunity, left the country, according to court documents.

It is not known who told Erb to leave and what her superiors at the embassy were told about the circumstances of her departure.

Hours after FBI agents first confronted Pollard at work last Nov. 18, he alerted Joseph (Yossi) Yagur, a science consul based in New York who was then Pollard's chief handler, prosecutors said.

Pollard on Nov. 20 telephoned the security officer at the Israeli Embassy, according to prosecutors, and after reciting the names of his Israeli handlers, asked that asylum be arranged.

The next day, Nov. 21, Pollard again called the security officer who told him to come to the embassy if he could "shake" his FBI surveillance, prosecutors said. Pollard was arrested outside the embassy that day by FBI agents who followed him there.

The identity of the Israeli security officer has never been made public. It is also not known whether the security officer discussed Pollard's request for asylum with anybody else in the embassy.

Some U.S. officials over the last two weeks have insisted that the new information developed by investigators since last December raises questions about Israeli claims that the Pollard case was a "renegade" operation unauthorized by top Israeli political leaders.

These officials said their doubts about the Israeli account arise in part from disclosures that Pollard's Israeli contacts paid him more than $45,000, opened the Swiss bank account for him under a fake name and planned to deposit $30,000 each year for the next 10 years, and arranged for two overseas trips, including a stop in Israel, to entertain him and provide him with specific instructions on what kinds of documents were needed.

"In every intelligence operation you have a built-in plausible deniability," said one U.S. official involved in counterintelligence. "You can't have the number of people, the quality of intelligence Pollard provided , the amount of money involved and the amount of time in an operation like this and have it be a so-called 'rogue operation.' "

"I don't know that it was a renegade operation," said Sen. David F. Durenberger (R-Minn.), chairman of the Select Committee on Intelligence, which has been briefed on the case by Justice Department officials. "What we know today that we didn't know a year ago is that we need more information . . . . The investigation . . . is ongoing."