Mass fir­ings and forced res­ig­na­tions swept through the FDA on Tues­day, as part of thou­sands of planned job cuts at fed­er­al health agen­cies be­ing im­ple­ment­ed by the Trump ad­min­is­tra­tion.

Some em­ploy­ees who showed up to work at the FDA's main White Oak cam­pus on Tues­day found out they had been fired when they at­tempt­ed to check in at se­cu­ri­ty, on­ly to find out that their badges no longer worked and their jobs were gone. They were then es­cort­ed by se­cu­ri­ty to col­lect their be­long­ings. The scenes were de­scribed to End­points News by sev­er­al peo­ple who wit­nessed them, and re­quest­ed anonymi­ty.

Oth­ers, such as CDER Of­fice of New Drugs Di­rec­tor Pe­ter Stein, were of­fered a new, hasti­ly cre­at­ed role in a dif­fer­ent de­part­ment — or the choice to quit.

WASH­ING­TON — The size and scope of the FDA that be­gan Tues­day won’t be the same as the day nears a bru­tal con­clu­sion for agency staffers that were laid off or forced to re­sign.

Sit­ting in a cor­ner of­fice clos­er to the pow­er bro­kers that craft­ed the re­struc­tur­ing, BIO CEO John Crow­ley tried not to cat­a­stro­phize.

“It’ll be a chal­lenge,” he said in an ex­clu­sive in­ter­view with End­points News. “We take the FDA as we find it and this is the FDA we have to­day.”

Few ar­eas of the agency were spared as part of the Trump ad­min­is­tra­tion's sweep­ing cuts. Chief med­ical of­fi­cer Hi­lary Marston was fired; the head of the Of­fice of New Drugs, Pe­ter Stein, was placed on ad­min­is­tra­tive leave; and the Of­fice of Me­dia Af­fairs was dec­i­mat­ed by cuts. There were deep cuts at the FDA’s Of­fice of Man­u­fac­tur­ing Qual­i­ty and im­muno-on­col­o­gy staff with­in CBER.

On Tues­day, drug dis­cov­er­er and biotech en­tre­pre­neur Al­pha Lee told sci­en­tists at a chem­istry meet­ing about a new mol­e­cule to com­bat the Zi­ka virus. There are no treat­ments de­signed to stop the mos­qui­to-borne in­fec­tion, which can cause birth de­fects. Af­ter three years of work, Lee and a team of col­lab­o­ra­tors had made a com­pound that shut down an en­zyme that’s es­sen­tial for Zi­ka virus repli­ca­tion.

But his ex­cite­ment was short-lived. Af­ter the con­fer­ence ses­sion end­ed, Lee checked his email and saw that the $67 mil­lion fed­er­al fund­ing sup­port­ing the work and sev­er­al oth­er an­tivi­ral pro­grams had been ter­mi­nat­ed.

“The end of the pan­dem­ic pro­vides cause to ter­mi­nate COVID-re­lat­ed grant funds. These grant funds were is­sued for a lim­it­ed pur­pose: to ame­lio­rate the ef­fects of the pan­dem­ic. Now that the pan­dem­ic is over, the grant funds are no longer nec­es­sary,” said the email, which was re­viewed by End­points News.

A top of­fi­cial pushed out over vac­cines. Se­nior staff head­ing for the ex­it. Thou­sands of work­ers tar­get­ed for fir­ing. A new com­mis­sion­er who has yet to vis­i­bly take charge. And an HHS sec­re­tary whose views on vac­cines run counter to es­tab­lished sci­ence.

Af­ter sev­er­al tu­mul­tuous weeks at the FDA, many in­side and out­side the agency are won­der­ing: What could come next?

Cen­ter for Bi­o­log­ics Eval­u­a­tion and Re­search Di­rec­tor Pe­ter Mark­s' Fri­day ex­it was just the high­est-pro­file of a num­ber of key staff de­par­tures. Oth­er top of­fi­cials who have left in the past month in­clude Lo­la Fashoyin-Aje, head of cell and gene ther­a­py clin­i­cal eval­u­a­tion, Heather Lom­bar­di, head of cell ther­a­pies, Heather Erd­man, as­so­ciate di­rec­tor of qual­i­ty as­sur­ance, and Vaishali Popat, branch chief in cell and gene ther­a­pies, ac­cord­ing to sources.

The de­par­ture of one of the FDA’s high­est-pro­file reg­u­la­tors, whose ca­reer was de­fined by ad­vanc­ing new tech­nolo­gies to pa­tients, rat­tled in­vestors and com­pa­nies who were al­ready feel­ing in­se­cure.

Fri­day’s shock ex­it of Pe­ter Marks, the di­rec­tor of the Cen­ter for Bi­o­log­ics Eval­u­a­tion and Re­search, was met by dis­may across the in­dus­try. Marks was best known by the broad­er pub­lic for his work on Covid-19 vac­cines dur­ing the pan­dem­ic — which made him a tar­get for HHS Sec­re­tary Robert F. Kennedy Jr., who has tak­en mul­ti­ple steps to un­der­mine vac­cine re­search and trust.

But as the head of the bi­o­log­ics cen­ter, Marks wa