ftz-f1¹⁷/Df(3L)Cat animals display defects in pupation. During prepupal development the abdominal air bubble shows delayed or complete failure of displacement. Head eversion defects, generating a cryptocephalic phenotype, are also observed. The third thoracic legs are short and malformed.

In ftz-f1¹⁷/ftz-f1¹⁹ and ftz-f1¹⁷/Df(3L)Cat animals the shape and size of 0-h prepupal leg imaginal discs are normal. The imaginal discs in 6-h prepupae are also normal. Mutant leg discs also show the successful transformation of cells from anisometric to isometric in the basitarsal and tibial segments. ftz-f1¹⁷/Df(3L)Cat mutant prepupae exhibit normal leg development until just before head eversion, when a dramatic anterior translocation of the leg occurs in wild-type. The legs in mutant animals make a slight anterior shift at 17 hours after puparium formation (APF) reaching a most anterior position at 17:12 APF. Unlike controls, the mutant legs are never drawn far enough toward the anterior to align with the eye-antennal imaginal discs. Final leg and wing elongation by 17:18 APF and is complete by 17:30 . Throughout the final elongation process, the mutant legs remain bent and never straighten as in controls. More bending in the mutant is observed up to about 18h APF. refinement is delayed in the mutant, beginning around 21:00 in the mutant, as opposed to around 19h APF in controls, but appear to proceed normally. All subsequent leg development in the mutant appears to occur normally. All subsequent leg development in the mutant occurs normally at the proper time. At 50h APF the mutant legs appear normally segmented, but are short, thick and bent. In mutant animals the gas bubble translocation and expulsion normally seen in wild-type between 4h and 12h APF is incomplete. A translucent area persists in the mid abdominal region occupied by the gas bubble, indicating the presence of residual gas, not present in controls. This gas is present until much later, when the mouthparts have been detached. Mutant animals also show defects in posterior retraction of the prepupal body and anterior gas movement. Posterior retraction begins later in the mutant than in controls, and occurs sporadically in the mutant, eventually bringing the posterior tip of the abdomen to between denticle belts 8 and 9, but never past denticle belt 8. In mutant pupae the various movements seen in wild-type that detach the mouthparts and allow the head to evert fully are abnormal. Mutant animals fail to shorten their bodies during metamorphosis, though the length of the pupal case is unaffected. The defects seen in these mutants can be rescued to varying degrees by exposure to decreased external pressure.

In ftz-f1¹⁷/ftz-f1¹⁹ mutant pupae 24 after pupariation formation (APF), DNA degradation is blocked. The salivary glands possess large cytoplasmic vacuoles reminiscent of the cell morphology of wild-type 12 hour salivary glands. Adult head eversion occurs normally in these animals.

ftz-f1¹⁷/ftz-f1¹⁹ mutant salivary glands are arrested prior to the onset of cell death and possess large eosin positive vacuoles, intact plasma membranes and banded polytene chromosomes - phenotypes associated with delaying salivary gland programmed cell death due to a failure in the onset of autophagy.

Some animals survive until puparium formation. Late third instar larvae pupariate and show early prepupal development that is indistinguishable from control animals: they evert their anterior spiracles and shorten normally, pupal cases sclerotize and tan, the dorsal air bubble forms and trachea show characteristic lateral movements. These factors indicate the response to the larval ecdysone pulse is normal. The response to the prepupal ecdysone pulse is abnormal. 10% survive to adulthood, 34% die as pharate adults with short or malformed legs, 39% complete head eversion and then arrest development as early pupae with bloated and malformed legs (surviving for 7-10 days before becoming necrotic), 18% fail head eversion and have severely distorted legs but continue most aspects of pupal development, though the mouthhooks remain attached to the body and the head differentiates within the thorax to produce a cryptocephalic phenotype. Legs of mutants do not show segmentation abnormalities, but mutant legs are shorter, wider and more kinked than wild type. Bristle development is incomplete on the femur and tibia. In many mutants the salivary glands do not undergo their programmed cell death.