Transmission spectroscopy is a powerful tool for understanding exoplanet atmospheres. At optical wavelengths, this technique makes it possible to infer the composition and the presence of aerosols in the atmosphere. However, unocculted stellar activity can result in contamination of atmospheric transmission spectra by introducing spurious slopes and molecular signals. We aim to characterise the atmosphere of the transiting exoplanet WASP-69b, a hot Jupiter orbiting an active K star, and characterise the activity levels of the host star. We obtained three nights of spectrophotometric data with the FORS2 instrument on the VLT, covering a wavelength range of 340-1100\,nm. These were divided into 10\,nm binned spectroscopic light curves, which were fit with a combination of Gaussian processes and parametric models to obtain a transmission spectrum. We performed retrievals on the full spectrum with combined stellar activity and planet atmosphere models. We directly detect a facula in the form of a hot-spot-crossing event in one of the transits and indirectly detect unocculted faculae through an apparently decreasing radius towards the blue end of the transmission spectrum. We determine a facula temperature of $ $\,K for the former and a stellar coverage fraction of around 30<!PCT!> with a temperature of $ T=+231 for the latter. The planetary atmosphere is best fit with a high-altitude cloud deck at 1.4\,mbar that mutes atomic and molecular features. We find indications of water and ammonia with $ and log(NH$_3$)=$-3.4^ $ , respectively, and place 3 upper limits on TiO $) and K ($<10^ $). We see a lack of evidence of Na, which we attribute to the presence of clouds. The simultaneous multi-wavelength observations allow us to break the size--contrast degeneracy for facula crossings, meaning we can obtain temperatures for both the directly and indirectly detected faculae, which are consistent with each other.
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