Intense, high energy stellar irradiation is believed to control the atmospheric mass loss of short-period planets. These effects are most dramatic in the early stages of planetary evolution, when young stars produce higher levels of X-ray and Ultraviolet radiation, and exhibit more short-term high-energy bursts of radiation called stellar flares. Observing how close-in planets react to these environments is key to understanding planetary evolution. In this dissertation, I present four studies of young stellar activity and planetary atmospheres as viewed in UV, optical, and infrared wavelengths. First, I present a study of stellar flares from five hours of Hubble Space Telescope Cosmic Origins Spectrograph (1070-1360AA) observations of the ~25 Myr M dwarf AU Microscopii (AU Mic). I detect 12 flares in the far-UV "white-light" curve with energies ranging from 10^29 - 10^32 ergs. To contextualize these observations for AU Mic b and c, I estimate the additional atmospheric mass lost in the presence of flares. I find the atmospheric mass-loss is ~10^ g/s, with instantaneous increases by up to 10^12 g/s in the presence of superflares. Second, I present a study of ground-based optical observations of a transit of V1298 Tau c, a 30-40 Myr super-Neptune planet. I observed a full transit with Gemini-North/GRACES and measure an obliquity of lambda = 5° +\- 15° via Doppler tomography. The tomographic signal is only seen in the chromospherically driven core of the Ca II IRT, which may be the result of star-planet interactions. I find that excess absorption of the H-alpha line decreases smoothly during the transit. While this could be a tentative detection of hot gas escaping the planet, I show this variation can also be explained by the presence of surface heterogeneities. Third, I present a survey of stellar flares in optical/infrared broad-band observations from the Transiting Exoplanet Survey Satellite (TESS) I developed and applied a novel convolutional neural network of flare detection to 3200 young stars to evaluate flare rates as a function of age and spectral type. I find that flare rates and amplitudes decrease for stars t_age > 50 Myr across all temperatures Teff >= 4000 K, while stars from 2300 <= Teff < 4000 K show no evolution across 800 Myr. Additionally, I applied this new network to all stars observed during the TESS primary mission. Last, I present the first transmission spectrum of the hot-Saturn WASP-39b as observed with JWST Near InfaRed Imager and Slitless Spectrograph. The spectrum spans 0.6 - 2.8 um in wavelength and reveals multiple water absorption bands, the potassium resonance doublet, as well as signatures of clouds. I find the atmospheric composition of WASP-39b, favors a heavy element enhancement of ~10 - 30x the solar value, a sub-solar carbon-to-oxygen ratio, and a solar-to-super-solar potassium-to-oxygen ratio. The observations are best explained by wavelength-dependent, non-gray clouds with inhomogeneous coverage of the planet's terminator.