Deformed intrusive rocks are common throughout the footwall map units. These intrusive rocks occur as thin (<1–3 m), sheet-like to irregular bodies that have sharp contacts with their host metamorphic rocks. An extended range in composition from mafic to felsic characterizes these igneous rocks. Typical examples are gabbro–quartz diorite, biotite granodiorite–monzogranite orthogneiss, and muscovite leucogranite orthogneiss. Similar intrusive rocks occur in the adjacent Gordon Creek quadrangle and have been dated as middle Eocene. Pegmatitic leucogranite is also widespread in the footwall units and is correlated with early Oligocene–Late Cretaceous leucogranite common throughout the RM-EHR core complex. Small areas of granitic orthogneiss of Secret Peak, biotite-muscovite monzogranitic orthogneiss, and quartz diorite of Rattlesnake Canyon are locally mapped separately.

The unmetamorphosed strata of the hanging wall include rocks ranging from the Pennsylvanian–Mississippian Diamond Peak Formation to the Early Triassic Thaynes Formation. One small exposure of middle Eocene volcanic and volcaniclastic rocks is also part of the hanging-wall sequence. Various paleontological age data have been determined from the unmetamorphosed sedimentary sequence, including from megafossils, fusulinids, and conodonts. The conodonts provide age determinations and thermal histories through conodont alteration indices (CAIs). High CAIs (5–6) from the Pennsylvanian Ely Limestone (*e) indicate that the host rock reached 400–500 ºC. These temperature determinations are interpreted to be related to hot fluids generated from the metamorphic and igneous footwall of the detachment-fault system.

The metamorphic and igneous complex forming the footwall records a complex history of penetrative deformation, polyphase folding, and crystal-plastic deformation in the mylonitic shear zone. Pre-mylonitic folds are well-developed in the southwestern corner of the quadrangle. These folds typically fold an earlier foliation with hinge lines trending to the northwest–southeast and are locally overprinted by the mylonitic shear zone. The formation age of the pre-mylonitic foliation and folds is uncertain, but it may be Late Cretaceous synchronous with upper-amphibolite facies metamorphism dated by U-Pb on monazite. Upper-amphibolite facies conditions for the metamorphic rocks of the footwall are based on the presence of the metapelitic assemblage: quartz + biotite + sillimanite + plagioclase + muscovite + garnet + zircon. Two metapelite samples from the southwestern corner of the Secret Valley quadrangle in the _Zpmi unit yielded ~4 kb and ~600 ºC for the P-T (pressure and temperature) conditions based on thermobarometric data during regional metamorphism. Calc-silicate rocks having hornblende + diopside + garnet assemblages also support upper-amphibolite facies conditions for the metamorphism of the metasedimentary rocks. U-Pb monazite ages from the _Zpmi unit suggest a Late Cretaceous age for the upper-amphibolite facies metamorphism.

The younger mylonitic shear zone is characterized by a penetrative foliation and elongation lineation (stretching lineation) that typically trends west-northwest–east-southeast. Locally, this lineation is folded by post-mylonitic folds that typically show vergence to the west. These folds are interpreted as Oligocene and related to the shear deformation characteristic of the mylonitic shear zone. Microstructures in the mylonitic rocks such as grain-boundary migration, subgrain rotation, recrystallization of quartz, and asymmetric porphyroclasts indicate crystal-plastic deformation. Thermobarometric data from mylonitic rocks in the adjacent Tent Mountain quadrangle indicate P-T conditions of 3.1–3.7 kb and 580–620 ºC. Mylonitization ended by ~29–23 Ma based on published geochronologic and thermochronologic data. Thus, age and P-T estimates suggest that the metamorphic rocks in the Secret Valley quadrangle reflect upper-amphibolite facies metamorphism in the Late Cretaceous followed by early Oligocene mylonitization. The mylonitic shear zone was interpreted to reflect an early part of exhumation of the footwall of the detachment-fault zone.

Scarce outcrops of the middle Miocene Humboldt Formation are mapped in the northwestern corner of the quadrangle. Associated with the Humboldt Formation are rhyolite exposures, including a vitrophyre that yielded a date of 15 ± 1.5 Ma by the K-Ar technique on sanidine and a rhyolite flow that yielded an ⁴⁰Ar/³⁹Ar age of 15.37 Ma on anorthoclase (see table 1).

Small exposures of Humboldt Formation are poorly exposed along the southwest margin of Secret Valley and in north Ruby Valley suggesting that the Humboldt Formation underlies these topographic features. Exposures of the Humboldt Formation, more extensively exposed in the adjacent Heelfly Creek quadrangle, have been mapped as unconformably deposited on Paleozoic sedimentary rocks as well as units in the metamorphic and igneous complex. The basal contact of the Humboldt Formation in the Secret Valley quadrangle is poorly exposed. However, based on the geologic mapping in the Heelfly Creek quadrangle, it is also mapped here as an unconformity. If this is the correct interpretation, the RM-EHR detachment fault and mylonitic shear zone were denuded prior to the middle Miocene. Cobbles of metasedimentary and deformed metaigneous rocks in the Humboldt Formation support this interpretation.

Normal faults accommodate offset of the mylonitic shear zone as well as the RM-EHR detachment-fault zone. A normal fault is exposed east of Secret Pass in the ‘Secret Hills’. This unnamed fault accommodated downdrop of the undivided Lower Permian sedimentary rocks in the hanging wall of the RM-EHR detachment fault. This fault loses displacement farther north in Secret Valley. The Poison Canyon fault is an en echelon normal fault that is the important range-front normal fault in the Secret Valley quadrangle. It is estimated that the Poison Canyon fault has about one km of displacement along it. It can be traced north into the Tent Mountain quadrangle, where it loses displacement. These normal faults are interpreted to be post–Humboldt Formation (middle Miocene).

The youngest map units in the Secret Valley quadrangle include a variety of Quaternary deposits: alluvial-fan and stream deposits (Qfy, Qfi, Qfo, and QToa), glacial deposits (Qgm and Qgo), colluvium (Qc), and landslide deposits (Qls).