Looking back I can see many nice clues. Thanks to the setter for a very enjoyable puzzle.
Clues are blue, with definitions underlined. Answers are in BOLD CAPS, then wordplay. (ABC*) means 'anagram of ABC'. Deletions are in [square brackets].
1 Novel about British deposing leader in holy city (7)
REBECCA: RE, B[m]ECCA.
5 Got involved and won prize in audition (7)
MEDDLED: “in audition”, sounds like “medaled”.
9 Bird seed gets inside power tool (9)
SANDPIPER: PIP inside SANDER.
10 Scoundrel fried seafood, leaving tail (5)
SCAMP: the seafood is SCAMP[i].
11 Maiden one introduced to church leader (5,8)
FIRST MINISTER: FIRST (maiden), I (one) in MINSTER. Leaders of governments in places like Scotland, Wales and Northern Ireland.
13 Country-lovers bringing group of three pets round (8)
PATRIOTS: PATS (pets) around TRIO.
15 Sons in manor surprisingly free with money? (6)
RANSOM: anagram (“surprisingly”) of (MANOR*), with S (son) inserted. Tricky definition, in that “free” and “ransom” are used as verbs.
17 Overdue books waiting to be discovered (6)
LATENT: LATE, NT.
19 Bad one in brawl with Mr Barker (8)
DOBERMAN: anagram (“in brawl”) of (BAD ONE MR*). Once I knew the last letter was “N”, I spent a while looking for words ending with RON. Nicely disguised definition.
22 Flyer restricted lines about a term in slammer (9,4)
SECRETARY BIRD: SECRET (restricted) RY (railway=lines) about A, then BIRD.
25 European trophies put back in bar (5)
ESTOP: E (European), then POTS put back. One of those words lawyers love.
26 Patience tried endlessly as oil wasted (9)
SOLITAIRE: anagram (“wasted”) of (TRIE- AS OIL*). The TRIE[d] is “endless”.
27 Departs before day is over, being stunned (7)
TASERED: D (departs), ERE, SAT (day), all “over” meaning backwards.
28 Pervert at hotel in course towards conflict (7)
WARPATH: WARP (pervert), AT, H.
1 Society in same old routine to deteriorate (4)
RUST: S (society) in RUT.
2 Good man associated with criminal image (7)
BENEFIT: BEN is the man today, E-FIT is the image.
3 Credit involves coarse person in illegal scheme (5)
CAPER: CR for credit, “involving” APE.
4 Old man making climb has little desire (8)
APPETITE: PA “climbing”, then PETITE.
5 People holding hands: one a legendary charmer (6)
MERLIN: MEN “holding” L, R, and I.
6 Policemen, drink consumed, separate and scatter (9)
DISSIPATE: DI’S are the policemen, SIP, ATE.
7 Loose slate on outbuildings (4-3)
LEAN-TOS: anagram (“loose”) of (SLATE ON*).
8 Behaviour left people in debt — billions lost (10)
DEPORTMENT: PORT and MEN in DE[b]T, which has lost B for “billions”.
12 Shot scene with a plot that twists (10)
OPALESCENT: anagram (“that twists”) of (SCENE A PLOT*). Well disguised definition.
14 Landlord's sly look up inside skirts (9)
INNKEEPER: PEEK “up”, INNER “skirts”. Assemble as instructed.
16 Person upset by meeting deep disappointment (4,4)
BODY BLOW: BOD, YB=“upset” BY, LOW.
18 Old history master understood our group (7)
TACITUS: TACIT, US.
20 Wine in varied amounts sent north (7)
MADEIRA: backwards hidden answer.
21 Approach news boss declared satisfactory (6)
PASSED: PASS, ED.
23 Bury Football Club at home in San Siro (5)
INTER: easy to guess San Siro is the home ground of Inter Milan.
24 Certain notes hard to harmonise (4)
MESH: ME’S are the notes, H for hard.