The F.B.I. agreed today to pay a settlement of more than $1.16 million to the agent who brought about an overhaul of its crime laboratory. The agent, Frederic Whitehurst, who is a chemist, returned to work from a yearlong suspension today and then voluntarily resigned as required by the deal to settle part of his lawsuit against the bureau. In the 16-page settlement, a copy of which was obtained by The Associated Press, the Federal Bureau of Investigation agreed to pay $1.166 million now to buy annuities that would pay the 50-year-old agent annual amounts equal to the salary and pension he would have earned had he kept working until the normal F.B.I. retirement age of 57. Under terms of the settlement, the bureau will also pay $258,580 in legal fees to Dr. Whitehurst's lawyers, and the Justice Department will drop all consideration of disciplinary action against him. For 10 years as the laboratory supervisor and once the bureau's top bomb residue expert, Dr. Whitehurst complained mostly in vain about laboratory practices. But his efforts finally led last April to a scathing 500-page study of the laboratory by the Justice Department's inspector general, Michael Bromwich. Mr. Bromwich sharply criticized the laboratory for flawed scientific work and inaccurate, pro-prosecution testimony in major cases, including the Oklahoma City and World Trade Center bombings. Mr. Bromwich recommended major changes and discipline for five agents.