*SPOILER WARNING* i accidentally found Solder. What all did i miss???

i was just at the part of Behind The Seven Seals when i needed to find the IPSF bodies and search them. decided i needed some more money and i went out looking for anomalies when i came upon this big military base. i said fuck it ill take the dude out front out and then headed inside & started sneaking up behind all these guys. thought i was doing some really cool stealth side mission or something when all ov the sudden i reach Solder's door and my knife goes away. this caught me off gaurd and then all of the sudden the cutscene starts playing and im just like WHAT THE FUUUUCK. did i miss any good loot? any crucial parts to the story?