This is the last trip to the center of the Zone, the one from SoC, because the scientist at Yantar said Strelok took his psy-protection prototype thingie. Ring any bells?

Streloks second trip, that protection is a early unstable prototype to avoid a bit of those PSI-Emissions but it's nowhere near as strong as during his third trip where he went straight to the "brain schorcher" itself and shut it down, plus his third trip was from the military warehouses trough the outside of Red Forest and into Pripyat whereas his second trip appears to have been from deeper within Red Forest and trough the town of Limansk (Which doesn't actually exist in reality whereas Pripyat is a real town.)

It should make a bit more sense when you complete the game.
(It's a bit confusing at times I admit and it took a few replays for me to understand everything about Shadow of Chernobyl's story.)

This is more indepth and contains heavy spoilers but.

Strelok and his groups (Fang and Ghost) first trip to the center of the zone triggers a massive "emission" or blowout as it's also known as altering much of the zone, Strelok at this time appears to be mainly after valuable artifacts and the so called "Wish Granter" rumored to be at the center. (Everyone knows the center is the NPP but noone has managed to get close until Strelok succeeded in going past the Brain Scorcher.)

However the group encounters a code-locked door (This section is referred to in various audio logs you'll find during the Shadow of Chernobyl story.) and decides to leave the Wish Granter alone for now, group then leaves the NPP and the blowout scatters them.
(And in the Marshes a nondescript mercenary named Scar gets seriously affected due to this "emission" and joins with a group called Clear Sky to attempt to find the person who has breached the balance in the zone by reaching the center.

Strelok and his group now prepare a second expedition to the center most likely not knowing that the resulting emission could destroy everything in the zone but they also have a decoder for that door this time.
(Meanwhile Scar isn't far behind and learns more and more about Strelok and his group.)

Scar, after being aided by the scientists at lake Yantar manages to pass the PSI-Emitter there and can now travel trough to the center and manages this with the help of the Clear Sky faction.

CLEAR SKY SPOILERS BELOW!

Scar and Strelok end up in a running battle outside the NPP or rather on the roof of it while Clear Sky deals with the Monolith troopers below, Strelok attempts to outrun Scar which is armed with a prototype EMP like rifle that can destroy his PSI-Protection and render him vulnerable, unfortunately just as Scar catches up to Strelok and disables his protection device a big blowout occurs and destroys most of the forces in the area thus totally obliterating the Clear Sky faction though some members might still be active as scientists in other areas of the Zone.

The survivors of this event are brought into the NPP where a series of tests and brainwashing slowly destroys their minds and converts them to Monolith soldiers, among those are Scar and ironically Strelok himself whom both survived the emission.

STALKER SPOILERS BELOW!

In a further sense of irony Strelok himself is given the objective to find and kill Strelok and is sent via death truck back into the zone, truck hits a anomaly and only Strelok survives thanks to a passing Stalker and the help of Sidorovich but that brainwashing has damaged his memory.

After a series of trips trough various locations Strelok/Marked One as he is now known as learns about his previous expeditions and in the end meets with a guy known as "Doc" who explains the last of his previous journey.

Strelok now manages to disable both the Yantar device and Brain Scorcher creating a rush for the center as several active groups battle for the many valuable resources such as anomalies that might be located in areas behind there.

Another blowout puts an end to this as most forces are destroyed by it but Strelok manages to reach safety in the actual NPP and depending on how you play he either makes a wish at the "Wish Granter" such as "I want to be rich" and is killed by it or he disables the lock on the door and either joins the mysterious C-consciousness to keep the zone balanced and in order or totally destroys them and with them dead he probably destroyed most of the zone as well as there's no longer anything keeping that force in control - the so called No-Sphere which a group of scientist tampered with in a research lab near the NPP only to bring about the second explosions and create the Zone.
(This is thus Streloks third and last trip to the center, unsure how a sequel will deal with this but if he destroyed those guys then the zone was probably pretty unstable for quite some time afterwards and if he joined them it was probably not that different from before but a bit more "stable" - probably the same result if he died with the Wish Granter.